From dca14c5486fe2b1de4754d4b486032517ca2037b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 16 Oct 2024 13:59:48 +0100 Subject: [PATCH 01/82] Bump versions back to 3.17.0 after release --- CHANGELOG.md | 7 +++++++ nextflow.config | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 13 files changed, 28 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fe18aecee..a9236eb9d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + +### Credits + +### Enhancements & fixes + + ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 ### Credits diff --git a/nextflow.config b/nextflow.config index 496a9429f..84ef3cabf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -327,7 +327,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.16.1' + version = '3.17.0dev' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c9981b3d1..ea663624c 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -227,7 +227,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index b14b204a7..9630b4c5d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -221,7 +221,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index dd6b9d23e..f6fe94c7e 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -44,7 +44,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -224,7 +224,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 4cc4ac925..215a901a4 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -56,7 +56,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -294,7 +294,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 2799bc339..a494f6029 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -1221,7 +1221,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 4b477e6a7..f10e886fe 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -140,7 +140,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -1435,7 +1435,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 0293e72fa..451c2918f 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -50,7 +50,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -367,7 +367,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 70b17efcb..476f26117 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -40,7 +40,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -169,7 +169,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index bfc0873a4..82acf3cfd 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -130,7 +130,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index d46ed0819..9d17e1f2d 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ @@ -1314,7 +1314,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.16.1" + "nf-core/rnaseq": "v3.17.0dev" } }, [ diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 260cc8c1d..9b8ee731a 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From 4336b2b37d3f7e45c5621699366e8372f9682aad Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 16 Oct 2024 14:02:11 +0100 Subject: [PATCH 02/82] Update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a9236eb9d..84abc9860 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes +- [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release + ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From f919609edce138ab498bbe0a4739f7239e5da9ea Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 16 Oct 2024 14:17:08 +0100 Subject: [PATCH 03/82] Prettier --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84abc9860..07cc4de8d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release - ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 ### Credits From d59ecf72d0fbd22bfe2c8d924b637ae6124bbb00 Mon Sep 17 00:00:00 2001 From: Pablo Date: Thu, 16 May 2024 17:09:32 +0200 Subject: [PATCH 04/82] appy changes for ARM Signed-off-by: Pablo --- modules/local/star_align_igenomes/main.nf | 2 +- modules/local/star_genomegenerate_igenomes/main.nf | 2 +- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bedtools/genomecov/environment.yml | 3 ++- modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 +- modules/nf-core/custom/getchromsizes/environment.yml | 2 +- modules/nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/dupradar/environment.yml | 2 +- modules/nf-core/fastp/environment.yml | 2 +- modules/nf-core/fastqc/environment.yml | 2 +- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 2 +- modules/nf-core/hisat2/align/environment.yml | 4 ++-- modules/nf-core/hisat2/build/environment.yml | 2 +- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 +- modules/nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/picard/markduplicates/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/qualimap/rnaseq/environment.yml | 2 +- modules/nf-core/rsem/calculateexpression/environment.yml | 5 +++-- modules/nf-core/rsem/preparereference/environment.yml | 5 +++-- modules/nf-core/rseqc/bamstat/environment.yml | 4 ++-- modules/nf-core/rseqc/inferexperiment/environment.yml | 4 ++-- modules/nf-core/rseqc/innerdistance/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionannotation/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionsaturation/environment.yml | 4 ++-- modules/nf-core/rseqc/readdistribution/environment.yml | 4 ++-- modules/nf-core/rseqc/readduplication/environment.yml | 4 ++-- modules/nf-core/rseqc/tin/environment.yml | 4 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/samtools/flagstat/environment.yml | 4 ++-- modules/nf-core/samtools/idxstats/environment.yml | 4 ++-- modules/nf-core/samtools/index/environment.yml | 4 ++-- modules/nf-core/samtools/sort/environment.yml | 4 ++-- modules/nf-core/samtools/sort/main.nf | 1 - modules/nf-core/samtools/stats/environment.yml | 4 ++-- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/star/align/environment.yml | 8 ++++---- modules/nf-core/star/genomegenerate/environment.yml | 8 ++++---- modules/nf-core/stringtie/stringtie/environment.yml | 2 +- modules/nf-core/subread/featurecounts/environment.yml | 2 +- .../summarizedexperiment/environment.yml | 2 +- modules/nf-core/trimgalore/environment.yml | 4 ++-- modules/nf-core/tximeta/tximport/environment.yml | 2 +- modules/nf-core/ucsc/bedclip/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/umitools/dedup/environment.yml | 2 +- modules/nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 6 +++--- nextflow.config | 2 +- workflows/rnaseq/main.nf | 2 +- 58 files changed, 85 insertions(+), 83 deletions(-) diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 32f3cac29..22981ed06 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 814bc7c8c..c36025b05 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "bioconda::star bioconda::samtools conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 4c6db6276..2e7bb8194 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bbmap=39.01 + - bioconda::bbmap diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 8fbe20c31..4d4e55eaf 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,7 +1,8 @@ name: bedtools_genomecov channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.31.1 + - bioconda::bedtools diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 954e8913d..b02bf1cfe 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -27,7 +27,7 @@ process BEDTOOLS_GENOMECOV { if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } - def sort_cmd = sort ? '| bedtools sort' : '' + def sort_cmd = sort ? '| sort -k1,1 -k2,2n' : '' def prefix = task.ext.prefix ?: "${meta.id}" if (intervals.name =~ /\.bam/) { diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121f..7a9bebebf 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index 5e757bf4c..a801ae936 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::python=3.9.5" + - conda-forge::python" diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 2a01695f1..7555c59ee 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.16.1 + - bioconda::samtools diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index a859dc881..638bc4a75 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - python=3.9.5 + - python diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index 58b2bf11d..0f6aa3d2b 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-dupradar=1.32.0" + - "bioconda::bioconductor-dupradar" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e664..6970ba186 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fastp=0.23.4 + - bioconda::fastp diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a9..936bf0896 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fastqc=0.12.1 + - bioconda::fastqc diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index c588de38a..71231aa8b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::fq=0.9.1 + - bioconda::fq diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 5398f71c5..17e6bb6cb 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gffread=0.12.1 + - bioconda::gffread diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 25910b340..d05be27a8 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::sed diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 0c1415f94..f10c74a40 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 - - bioconda::samtools=1.16.1 + - bioconda::hisat2 + - bioconda::samtools diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index 2e67cd3ea..78fa8b257 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 + - bioconda::hisat2 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index 4b03e5e46..4ae5a0986 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::hisat2=2.2.1 + - bioconda::hisat2 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 471b006a8..5ddd1ce3f 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index c2d6306bb..8b95f28f3 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67e..7c7e1e5d7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 58b795f54..7e0b0b34c 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 57b8b9c67..7d8613bcc 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::preseq=3.1.2 + - bioconda::preseq diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 590ae85f7..f1f0b04db 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::qualimap=2.3 + - bioconda::qualimap diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b811fa6fe..47d0158ab 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,8 +1,9 @@ name: rsem_calculateexpression channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::rsem=1.3.3 - - bioconda::star=2.7.10a + - bioconda::rsem + - bioconda::star diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index c80e69106..c4ef537cb 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,8 +1,9 @@ name: rsem_preparereference channels: + - seqera - conda-forge - bioconda - defaults dependencies: - - bioconda::rsem=1.3.3 - - bioconda::star=2.7.10a + - seqera::rsem + - seqera::star=2.6.1d diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index e960c9943..2894094ee 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index 78215985a..e6affc939 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index fb6e9e925..bb7838a3f 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index 35276b715..9c43c0d5a 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index 7b9cc4fa7..7e2607545 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index 59be9fa88..dcdc0defd 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index c99f107a1..3600c7054 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index 288da4300..f24194b5f 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::rseqc=5.0.3 - - conda-forge::r-base>=3.5 + - bioconda::rseqc + - conda-forge::r-base diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index a6607d964..29f762517 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 862667241..28439bdbe 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index bd57cb54d..cd58f431d 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 174973b88..5d0378237 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e506498..84b752bde 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 4d898e486..fbb6233ea 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index fc374f980..0aed6b796 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 67bb0ca40..74f55132b 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools + - bioconda::htslib diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index f40f9958d..369a72994 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::sortmerna=4.3.6 + - bioconda::sortmerna diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 8bd58cff5..f639ccfb0 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - conda-forge::gawk=5.1.0 + - bioconda::star + - bioconda::samtools + - bioconda::htslib + - conda-forge::gawk diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 791f255e5..1170105b5 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -4,7 +4,7 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - bioconda::star=2.7.10a - - conda-forge::gawk=5.1.0 + - bioconda::samtools + - bioconda::htslib + - bioconda::star + - conda-forge::gawk diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 7a0eccdb8..7c3a0158d 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index ca19439d7..812744486 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 252ace791..f97e7d943 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-summarizedexperiment=1.32.0" + - "bioconda::bioconductor-summarizedexperiment" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 17b39f4a5..234bca959 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::trim-galore=0.6.7 - - bioconda::cutadapt=3.4 + - bioconda::trim-galore + - bioconda::cutadapt diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 24b202222..4649d1759 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-tximeta=1.20.1" + - "bioconda::bioconductor-tximeta" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 571dc2749..ae7bcb0d1 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ucsc-bedclip=377 + - bioconda::ucsc-bedclip diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index f91e216f5..1e6658778 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index bc497824f..173040160 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index aab452d1e..0d979b32c 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index dbb1bde77..cf83ff218 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::umi_tools=1.1.5 + - bioconda::umi_tools diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb101..fbf281f50 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -6,6 +6,6 @@ channels: - defaults dependencies: - - conda-forge::grep=3.11 - - conda-forge::sed=4.7 - - conda-forge::tar=1.34 + - conda-forge::grep + - conda-forge::sed + - conda-forge::tar diff --git a/nextflow.config b/nextflow.config index ca0d3a7e6..1164e2542 100644 --- a/nextflow.config +++ b/nextflow.config @@ -123,7 +123,7 @@ params { // Max resource options // Defaults only, expecting to be overwritten - max_memory = '128.GB' + max_memory = '256.GB' max_cpus = 16 max_time = '240.h' diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index b679a4b34..13c5bf118 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -142,7 +142,7 @@ workflow RNASEQ { .reads .mix(ch_fastq.single) .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! From 4bdae48230c5b1bc9f8c0cdbdecce342f8ecb4cf Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:50:30 +0100 Subject: [PATCH 05/82] Fix up config --- conf/arm.config | 146 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 146 insertions(+) create mode 100644 conf/arm.config diff --git a/conf/arm.config b/conf/arm.config new file mode 100644 index 000000000..345e38efd --- /dev/null +++ b/conf/arm.config @@ -0,0 +1,146 @@ +// Apply software overrides for ARM compatibility + +withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' +} + +withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' +} + +withName: 'BBSPLIT' { + conda = 'bioconda::bbmap' +} + +withName: 'BEDTOOLS_GENOMECOV' { + conda = 'bioconda::bedtools' +} + +withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils' +} + +withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'conda-forge::python' +} + +withName: 'CUSTOM_GETCHROMSIZES' { + conda = 'bioconda::samtools' +} + +withName: 'CUSTOM_TX2GENE' { + conda = 'python' +} + +withName: 'DUPRADAR' { + conda = 'bioconda::bioconductor-dupradar' +} + +withName: 'FASTP' { + conda = 'bioconda::fastp' +} + +withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq' +} + +withName: 'GFFREAD' { + conda = 'bioconda::gffread' +} + +withName: 'GUNZIP' { + conda = 'conda-forge::sed' +} + +withName: 'HISAT2_ALIGN' { + conda = 'bioconda::hisat2 bioconda::samtools' +} + +withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + conda = 'bioconda::hisat2' +} + +withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto' +} + +withName: 'MULTIQC' { + conda = 'bioconda::multiqc' +} + +withName: 'PICARD_MARKDUPLICATES' { + conda = 'bioconda::picard' +} + +withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq' +} + +withName: 'QUALIMAP_RNASEQ' { + conda = 'bioconda::qualimap' +} + +withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'bioconda::rsem bioconda::star' +} + +withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem seqera::star=2.6.1d' +} + +withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { + conda = 'bioconda::rseqc conda-forge::r-base' +} + +withName: 'SALMON_INDEX|SALMON_QUANT' { + conda = 'bioconda::salmon' +} + +withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { + conda = 'bioconda::samtools bioconda::htslib' +} + +withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna' +} + +withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' +} + +withName: 'STRINGTIE_STRINGTIE' { + conda = 'bioconda::stringtie' +} + +withName: 'SUBREAD_FEATURECOUNTS' { + conda = 'bioconda::subread' +} + +withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + conda = 'bioconda::bioconductor-summarizedexperiment' +} + +withName: 'TXIMETA_TXIMPORT' { + conda = 'bioconda::bioconductor-tximeta' +} + +withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore bioconda::cutadapt' +} + +withName: 'UCSC_BEDCLIP' { + conda = 'bioconda::ucsc-bedclip' +} + +withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig' +} + +withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + conda = 'bioconda::umi_tools' +} + +withName: 'UNTAR' { + conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' +} + From c9d616ba7c72eb0eae9ebeec5c44eaa9cd6529d2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:52:30 +0100 Subject: [PATCH 06/82] Reset environment ymls --- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bedtools/genomecov/environment.yml | 3 +-- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 +- modules/nf-core/custom/getchromsizes/environment.yml | 3 ++- modules/nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/dupradar/environment.yml | 2 +- modules/nf-core/fastp/environment.yml | 2 +- modules/nf-core/fastqc/environment.yml | 2 +- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gunzip/environment.yml | 4 +++- modules/nf-core/hisat2/align/environment.yml | 4 ++-- modules/nf-core/hisat2/build/environment.yml | 2 +- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 +- modules/nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/picard/markduplicates/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/qualimap/rnaseq/environment.yml | 2 +- modules/nf-core/rsem/calculateexpression/environment.yml | 5 ++--- modules/nf-core/rsem/preparereference/environment.yml | 5 ++--- modules/nf-core/rseqc/bamstat/environment.yml | 4 ++-- modules/nf-core/rseqc/inferexperiment/environment.yml | 4 ++-- modules/nf-core/rseqc/innerdistance/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionannotation/environment.yml | 4 ++-- modules/nf-core/rseqc/junctionsaturation/environment.yml | 4 ++-- modules/nf-core/rseqc/readdistribution/environment.yml | 4 ++-- modules/nf-core/rseqc/readduplication/environment.yml | 4 ++-- modules/nf-core/rseqc/tin/environment.yml | 4 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/samtools/flagstat/environment.yml | 4 ++-- modules/nf-core/samtools/idxstats/environment.yml | 4 ++-- modules/nf-core/samtools/index/environment.yml | 4 ++-- modules/nf-core/samtools/sort/environment.yml | 4 ++-- modules/nf-core/samtools/stats/environment.yml | 4 ++-- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/star/align/environment.yml | 8 ++++---- modules/nf-core/star/genomegenerate/environment.yml | 8 ++++---- modules/nf-core/stringtie/stringtie/environment.yml | 2 +- modules/nf-core/subread/featurecounts/environment.yml | 2 +- .../summarizedexperiment/environment.yml | 2 +- modules/nf-core/trimgalore/environment.yml | 4 ++-- modules/nf-core/tximeta/tximport/environment.yml | 2 +- modules/nf-core/ucsc/bedclip/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/umitools/dedup/environment.yml | 2 +- modules/nf-core/umitools/extract/environment.yml | 2 +- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 +- modules/nf-core/untar/environment.yml | 6 +++--- 52 files changed, 80 insertions(+), 80 deletions(-) diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 3a0ecdf34..dfd8936e1 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap + - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index d415ae6ec..5683bc05f 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,6 +1,5 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - bioconda::bedtools + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index d15cbda27..c7eb9bd1c 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::coreutils + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index fd1010315..1d80d11a9 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python" \ No newline at end of file + - conda-forge::python=3.9.5 diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 96b17c413..da2df5e43 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -2,4 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index f626c1c72..9f5f9fb9b 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python + - python=3.9.5 diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index ca8f5abef..fb16938d2 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-dupradar" + - "bioconda::bioconductor-dupradar=1.32.0" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index de3512e0a..26d4aca5d 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastp + - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 30e0b77e3..691d4c763 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fastqc + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index f28625955..eaba9339b 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fq + - bioconda::fq=0.9.1 diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 61b39921a..ee2398416 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::gffread \ No newline at end of file + - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 86c0feb98..c7794856d 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -2,4 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::sed \ No newline at end of file + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 75a1d7505..26c62a3bf 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 - - bioconda::samtools + - bioconda::hisat2=2.2.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index c2696c30e..afced7338 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index c2696c30e..afced7338 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hisat2 + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 6ccef310c..27be64918 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto + - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index 6ccef310c..27be64918 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto + - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 103b4c045..6f5b867b7 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc \ No newline at end of file + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 4dc4357d0..5f919a9a9 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard + - bioconda::picard=3.1.1 diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 06bec39d0..926d7aece 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::preseq + - bioconda::preseq=3.1.2 diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 28bab2f99..4fa5f4e8e 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::qualimap + - bioconda::qualimap=2.3 diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b29ff989b..bcf70fa9a 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,7 +1,6 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - bioconda::rsem - - bioconda::star + - bioconda::rsem=1.3.3 + - bioconda::star=2.7.10a diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index b70d9f18d..bcf70fa9a 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,7 +1,6 @@ channels: - - seqera - conda-forge - bioconda dependencies: - - seqera::rsem - - seqera::star=2.6.1d + - bioconda::rsem=1.3.3 + - bioconda::star=2.7.10a diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index b82581d16..304e38fcf 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::rseqc - - conda-forge::r-base + - bioconda::rseqc=5.0.3 + - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index b4e2d89de..471164faa 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon + - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index b4e2d89de..471164faa 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon + - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 55c7b199f..da2df5e43 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib \ No newline at end of file + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index 6fd5e7442..fab44081f 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sortmerna + - bioconda::sortmerna=4.3.6 diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 0084b66ae..e3d1c714d 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::star - - bioconda::samtools - - bioconda::htslib - - conda-forge::gawk + - bioconda::star=2.7.10a + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 6617b4720..38611dfa2 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools - - bioconda::htslib - - bioconda::star - - conda-forge::gawk + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 + - bioconda::star=2.7.10a + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 25e1a3810..0556de41a 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie + - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 43bff6526..7e919aa31 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread + - bioconda::subread=2.0.1 diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 24ce1dcde..dc4e6c936 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-summarizedexperiment" + - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index c83091ea1..f172c1b39 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::trim-galore - - bioconda::cutadapt \ No newline at end of file + - bioconda::cutadapt=3.4 + - bioconda::trim-galore=0.6.7 diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 5c5179f35..4b6df0cfe 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bioconductor-tximeta" + - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 8e6772864..94e825f03 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedclip + - bioconda::ucsc-bedclip=377 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index 7eca50fcc..a54fb8f16 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig + - bioconda::ucsc-bedgraphtobigwig=445 diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index 2d4e5317c..9f9e03c49 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::umi_tools + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 14e237118..c7794856d 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::grep - - conda-forge::sed - - conda-forge::tar \ No newline at end of file + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 From 9f640ab5a1b517a0bdd6cb43a9eac5a364edbc4b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:55:16 +0100 Subject: [PATCH 07/82] Reset main.nfs with software changes only --- modules/local/star_align_igenomes/main.nf | 2 +- modules/local/star_genomegenerate_igenomes/main.nf | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 7341d5778..7bda3df84 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 775afde95..4e2fcf6bf 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star bioconda::samtools conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 98cfd4c8e..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -27,7 +27,6 @@ process BEDTOOLS_GENOMECOV { if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } - // Sorts output file by chromosome and position using additional options for performance and consistency // See https://www.biostars.org/p/66927/ for further details def buffer = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : '' From 00cff4c8e48a4cd15bd3fdb9ab92c0bfb2ae141e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 12:58:29 +0100 Subject: [PATCH 08/82] Link sw configs to arm profile --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 496a9429f..525c6f4e1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -186,6 +186,7 @@ profiles { } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + includeConfig 'conf/arm.config' } singularity { singularity.enabled = true From f281e0b13f63fda6b7a984910ff5db8ce665d072 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 13:13:27 +0100 Subject: [PATCH 09/82] Add process block --- conf/arm.config | 294 ++++++++++++++++++++++++------------------------ 1 file changed, 148 insertions(+), 146 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 345e38efd..112cb66af 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,146 +1,148 @@ -// Apply software overrides for ARM compatibility - -withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' -} - -withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' -} - -withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' -} - -withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools' -} - -withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils' -} - -withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'conda-forge::python' -} - -withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools' -} - -withName: 'CUSTOM_TX2GENE' { - conda = 'python' -} - -withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar' -} - -withName: 'FASTP' { - conda = 'bioconda::fastp' -} - -withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq' -} - -withName: 'GFFREAD' { - conda = 'bioconda::gffread' -} - -withName: 'GUNZIP' { - conda = 'conda-forge::sed' -} - -withName: 'HISAT2_ALIGN' { - conda = 'bioconda::hisat2 bioconda::samtools' -} - -withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - conda = 'bioconda::hisat2' -} - -withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto' -} - -withName: 'MULTIQC' { - conda = 'bioconda::multiqc' -} - -withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard' -} - -withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq' -} - -withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap' -} - -withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'bioconda::rsem bioconda::star' -} - -withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem seqera::star=2.6.1d' -} - -withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc conda-forge::r-base' -} - -withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon' -} - -withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools bioconda::htslib' -} - -withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna' -} - -withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' -} - -withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie' -} - -withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread' -} - -withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment' -} - -withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta' -} - -withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore bioconda::cutadapt' -} - -withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip' -} - -withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig' -} - -withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - conda = 'bioconda::umi_tools' -} - -withName: 'UNTAR' { - conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' -} - +process { + + // Apply software overrides for ARM compatibility + + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' + } + + withName: 'BBSPLIT' { + conda = 'bioconda::bbmap' + } + + withName: 'BEDTOOLS_GENOMECOV' { + conda = 'bioconda::bedtools' + } + + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils' + } + + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'conda-forge::python' + } + + withName: 'CUSTOM_GETCHROMSIZES' { + conda = 'bioconda::samtools' + } + + withName: 'CUSTOM_TX2GENE' { + conda = 'python' + } + + withName: 'DUPRADAR' { + conda = 'bioconda::bioconductor-dupradar' + } + + withName: 'FASTP' { + conda = 'bioconda::fastp' + } + + withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq' + } + + withName: 'GFFREAD' { + conda = 'bioconda::gffread' + } + + withName: 'GUNZIP' { + conda = 'conda-forge::sed' + } + + withName: 'HISAT2_ALIGN' { + conda = 'bioconda::hisat2 bioconda::samtools' + } + + withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + conda = 'bioconda::hisat2' + } + + withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto' + } + + withName: 'MULTIQC' { + conda = 'bioconda::multiqc' + } + + withName: 'PICARD_MARKDUPLICATES' { + conda = 'bioconda::picard' + } + + withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq' + } + + withName: 'QUALIMAP_RNASEQ' { + conda = 'bioconda::qualimap' + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'bioconda::rsem bioconda::star' + } + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem seqera::star=2.6.1d' + } + + withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { + conda = 'bioconda::rseqc conda-forge::r-base' + } + + withName: 'SALMON_INDEX|SALMON_QUANT' { + conda = 'bioconda::salmon' + } + + withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { + conda = 'bioconda::samtools bioconda::htslib' + } + + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna' + } + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' + } + + withName: 'STRINGTIE_STRINGTIE' { + conda = 'bioconda::stringtie' + } + + withName: 'SUBREAD_FEATURECOUNTS' { + conda = 'bioconda::subread' + } + + withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { + conda = 'bioconda::bioconductor-summarizedexperiment' + } + + withName: 'TXIMETA_TXIMPORT' { + conda = 'bioconda::bioconductor-tximeta' + } + + withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore bioconda::cutadapt' + } + + withName: 'UCSC_BEDCLIP' { + conda = 'bioconda::ucsc-bedclip' + } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig' + } + + withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + conda = 'bioconda::umi_tools' + } + + withName: 'UNTAR' { + conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + } +} From f5208dd0e78762e51bb34740ecea16a5cfc40949 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 16:31:04 +0100 Subject: [PATCH 10/82] note pins --- conf/arm.config | 76 ++++++++++++++++++++++++++++++++++++------------- 1 file changed, 56 insertions(+), 20 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 112cb66af..d5cbad5b4 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -3,146 +3,182 @@ process { // Apply software overrides for ARM compatibility withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools conda-forge::gawk=5.1.0' + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools conda-forge::gawk=5.1.0' + conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' + conda = 'bioconda::bbmap' + // conda = 'bioconda::bbmap=39.01' } withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools' + conda = 'bioconda::bedtools::2.13.1' + //conda = 'bioconda::bedtools::2.13.1' } withName: 'CAT_FASTQ' { conda = 'conda-forge::coreutils' + //conda = 'conda-forge::coreutils=8.30' } withName: 'CAT_ADDITIONAL_FASTA' { conda = 'conda-forge::python' + //conda = 'conda-forge::coreutils=3.9.5' } withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools' + conda = 'bioconda::samtools=1.21' + //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' } withName: 'CUSTOM_TX2GENE' { - conda = 'python' + conda = 'python=3.13.0' + //conda = 'python=3.9.5' } withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar' + conda = 'bioconda::bioconductor-dupradar=1.32.0' + //conda = 'bioconda::bioconductor-dupradar=1.32.0' } withName: 'FASTP' { conda = 'bioconda::fastp' + //conda = 'bioconda::fastp=0.23.4' } withName: 'FQ_SUBSAMPLE' { conda = 'bioconda::fq' + //conda = 'bioconda::fq=0.9.1' } withName: 'GFFREAD' { conda = 'bioconda::gffread' + //conda = 'bioconda::gffread=0.12.7' } withName: 'GUNZIP' { conda = 'conda-forge::sed' + //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' } withName: 'HISAT2_ALIGN' { conda = 'bioconda::hisat2 bioconda::samtools' + //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' } withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { conda = 'bioconda::hisat2' + //conda = 'bioconda::hisat2=2.2.1' } withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { conda = 'bioconda::kallisto' + //conda = 'bioconda::kallisto=0.48.0' } withName: 'MULTIQC' { - conda = 'bioconda::multiqc' + conda = 'bioconda::multiqc=1.25.1' + //conda = 'bioconda::multiqc=1.25.1' } withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard' + conda = 'bioconda::picard=3.3.0' + //conda = 'bioconda::picard=3.1.1' } withName: 'PRESEQ_LCEXTRAP' { conda = 'bioconda::preseq' + //conda = 'bioconda::preseq=3.1.2' } withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap' + conda = 'bioconda::qualimap=2.3' + //conda = 'bioconda::qualimap=2.3' } withName: 'RSEM_CALCULATEEXPRESSION' { conda = 'bioconda::rsem bioconda::star' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } withName: 'RSEM_PREPAREREFERENCE' { conda = 'seqera::rsem seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc conda-forge::r-base' + conda = 'bioconda::rseqc=5.0.2 conda-forge::r-base' + //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' } withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon' + conda = 'bioconda::salmon=1.10.3' + //conda = 'bioconda::salmon=1.10.1' } withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools bioconda::htslib' + conda = 'bioconda::samtools=1.21 bioconda::htslib' + //conda = 'bioconda::samtools=1.20 bioconda::htslib' } withName: 'SORTMERNA' { conda = 'bioconda::sortmerna' + //conda = 'bioconda::sortmerna=4.3.6' } withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' } withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie' + conda = 'bioconda::stringtie=2.2.3' + //conda = 'bioconda::stringtie=2.2.1' } withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread' + conda = 'bioconda::subread=2.0.6' + //conda = 'bioconda::subread=2.0.1' } withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment' + conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' + //conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' } withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta' + conda = 'bioconda::bioconductor-tximeta=1.20.1' + //conda = 'bioconda::bioconductor-tximeta=1.20.1' } withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore bioconda::cutadapt' + conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' + //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip' + conda = 'bioconda::ucsc-bedclip=377' + //conda = 'bioconda::ucsc-bedclip=377' } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig' + conda = 'bioconda::ucsc-bedgraphtobigwig=445' + //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' + //conda = 'bioconda::umi_tools=1.1.5' } withName: 'UNTAR' { conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' } } From ea8b9e8be4657416a3041351718493af03bfd410 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 17 Oct 2024 17:23:49 +0100 Subject: [PATCH 11/82] Remove conda overrides that were having no impact --- conf/arm.config | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index d5cbad5b4..d73605e09 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -17,11 +17,6 @@ process { // conda = 'bioconda::bbmap=39.01' } - withName: 'BEDTOOLS_GENOMECOV' { - conda = 'bioconda::bedtools::2.13.1' - //conda = 'bioconda::bedtools::2.13.1' - } - withName: 'CAT_FASTQ' { conda = 'conda-forge::coreutils' //conda = 'conda-forge::coreutils=8.30' @@ -42,11 +37,6 @@ process { //conda = 'python=3.9.5' } - withName: 'DUPRADAR' { - conda = 'bioconda::bioconductor-dupradar=1.32.0' - //conda = 'bioconda::bioconductor-dupradar=1.32.0' - } - withName: 'FASTP' { conda = 'bioconda::fastp' //conda = 'bioconda::fastp=0.23.4' @@ -82,11 +72,6 @@ process { //conda = 'bioconda::kallisto=0.48.0' } - withName: 'MULTIQC' { - conda = 'bioconda::multiqc=1.25.1' - //conda = 'bioconda::multiqc=1.25.1' - } - withName: 'PICARD_MARKDUPLICATES' { conda = 'bioconda::picard=3.3.0' //conda = 'bioconda::picard=3.1.1' @@ -97,11 +82,6 @@ process { //conda = 'bioconda::preseq=3.1.2' } - withName: 'QUALIMAP_RNASEQ' { - conda = 'bioconda::qualimap=2.3' - //conda = 'bioconda::qualimap=2.3' - } - withName: 'RSEM_CALCULATEEXPRESSION' { conda = 'bioconda::rsem bioconda::star' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' @@ -147,31 +127,11 @@ process { //conda = 'bioconda::subread=2.0.1' } - withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { - conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' - //conda = 'bioconda::bioconductor-summarizedexperiment=1.32.0' - } - - withName: 'TXIMETA_TXIMPORT' { - conda = 'bioconda::bioconductor-tximeta=1.20.1' - //conda = 'bioconda::bioconductor-tximeta=1.20.1' - } - withName: 'TRIMGALORE' { conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } - withName: 'UCSC_BEDCLIP' { - conda = 'bioconda::ucsc-bedclip=377' - //conda = 'bioconda::ucsc-bedclip=377' - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=445' - //conda = 'bioconda::ucsc-bedgraphtobigwig=445' - } - withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' //conda = 'bioconda::umi_tools=1.1.5' From db02d992556f593a66b0d5da9718f519bb2934f0 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 09:45:44 +0100 Subject: [PATCH 12/82] Use different RSEQC pin --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index d73605e09..f8e288f9d 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -93,7 +93,7 @@ process { } withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc=5.0.2 conda-forge::r-base' + conda = 'bioconda::rseqc=5.0.4 conda-forge::r-base' //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' } From 4a8ed2bb00bff13cdef9f4470c4a95bead441542 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:28:04 +0100 Subject: [PATCH 13/82] update BEDGRAPHTOBIGWIG pin --- conf/arm.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/arm.config b/conf/arm.config index f8e288f9d..4f7772681 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -131,6 +131,11 @@ process { conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } + + withName: 'UCSC_BEDGRAPHTOBIGWIG' { + conda = 'bioconda::ucsc-bedgraphtobigwig=469' + //conda = 'bioconda::ucsc-bedgraphtobigwig=469' + } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { conda = 'bioconda::umi_tools' From b86a6f9d9fc3515865eb4aaa600882df6c893c80 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:37:14 +0100 Subject: [PATCH 14/82] Fix annotation --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index 4f7772681..4efeabdfe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -133,7 +133,7 @@ process { } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=469' + conda = 'bioconda::ucsc-bedgraphtobigwig=445' //conda = 'bioconda::ucsc-bedgraphtobigwig=469' } From 1b96eb886b80c4cba0691728a89a4f17dbc5a0ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 10:47:36 +0100 Subject: [PATCH 15/82] Don't think we need the RSEQC pin --- conf/arm.config | 5 ----- 1 file changed, 5 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4efeabdfe..37a6d1211 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -92,11 +92,6 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } - withName: 'RSEQC_BAMSTAT|RSEQC_INFEREXPERIMENT|RSEQC_INNERDISTANCE|RSEQC_JUNCTIONANNOTATION|RSEQC_JUNCTIONSATURATION|RSEQC_READDISTRIBUTION|RSEQC_READDUPLICATION|RSEQC_TIN' { - conda = 'bioconda::rseqc=5.0.4 conda-forge::r-base' - //conda = 'bioconda::rseqc=5.0.3 conda-forge::r-base>=3.5' - } - withName: 'SALMON_INDEX|SALMON_QUANT' { conda = 'bioconda::salmon=1.10.3' //conda = 'bioconda::salmon=1.10.1' From 4e5d7a38d2c6fe355eaebde60611ec4c5b21f188 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 14:26:45 +0100 Subject: [PATCH 16/82] correct ucsc --- conf/arm.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 37a6d1211..933dfc928 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -128,8 +128,8 @@ process { } withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=445' - //conda = 'bioconda::ucsc-bedgraphtobigwig=469' + conda = 'bioconda::ucsc-bedgraphtobigwig=469' + //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { From 902367e6cb02990d70c1583bf52ec6ecb70f3b91 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:25:21 +0100 Subject: [PATCH 17/82] Triage arm deps --- conf/arm.config | 229 +++++++++++++++++++++++++----------------------- 1 file changed, 121 insertions(+), 108 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 933dfc928..4a6f22e53 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,144 +1,157 @@ process { + // // Apply software overrides for ARM compatibility - - withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - } - - withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'bioconda::star bioconda::samtools=1.21 conda-forge::gawk=5.1.0' - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - } - - withName: 'BBSPLIT' { - conda = 'bioconda::bbmap' - // conda = 'bioconda::bbmap=39.01' - } - - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils' - //conda = 'conda-forge::coreutils=8.30' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'conda-forge::python' - //conda = 'conda-forge::coreutils=3.9.5' - } - + // + + //// Tested, working, module updates in progress on main dev branch + withName: 'CUSTOM_GETCHROMSIZES' { conda = 'bioconda::samtools=1.21' //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' } - + withName: 'CUSTOM_TX2GENE' { conda = 'python=3.13.0' //conda = 'python=3.9.5' } - - withName: 'FASTP' { - conda = 'bioconda::fastp' - //conda = 'bioconda::fastp=0.23.4' - } - - withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq' - //conda = 'bioconda::fq=0.9.1' - } - - withName: 'GFFREAD' { - conda = 'bioconda::gffread' - //conda = 'bioconda::gffread=0.12.7' - } - - withName: 'GUNZIP' { - conda = 'conda-forge::sed' - //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - } - - withName: 'HISAT2_ALIGN' { - conda = 'bioconda::hisat2 bioconda::samtools' - //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' - } - - withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - conda = 'bioconda::hisat2' - //conda = 'bioconda::hisat2=2.2.1' - } - - withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto' - //conda = 'bioconda::kallisto=0.48.0' - } - - withName: 'PICARD_MARKDUPLICATES' { - conda = 'bioconda::picard=3.3.0' - //conda = 'bioconda::picard=3.1.1' - } - - withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq' - //conda = 'bioconda::preseq=3.1.2' - } - - withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'bioconda::rsem bioconda::star' - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - } - - withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem seqera::star=2.6.1d' - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - } - + withName: 'SALMON_INDEX|SALMON_QUANT' { conda = 'bioconda::salmon=1.10.3' //conda = 'bioconda::salmon=1.10.1' } - + withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { conda = 'bioconda::samtools=1.21 bioconda::htslib' //conda = 'bioconda::samtools=1.20 bioconda::htslib' } - - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna' - //conda = 'bioconda::sortmerna=4.3.6' - } - - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star bioconda::samtools bioconda::htslib conda-forge::gawk' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + + withName: 'TRIMGALORE' { + conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' + //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' } - + withName: 'STRINGTIE_STRINGTIE' { conda = 'bioconda::stringtie=2.2.3' //conda = 'bioconda::stringtie=2.2.1' } - + withName: 'SUBREAD_FEATURECOUNTS' { conda = 'bioconda::subread=2.0.6' //conda = 'bioconda::subread=2.0.1' } - - withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' - //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' - } withName: 'UCSC_BEDGRAPHTOBIGWIG' { conda = 'bioconda::ucsc-bedgraphtobigwig=469' //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } - - withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - conda = 'bioconda::umi_tools' - //conda = 'bioconda::umi_tools=1.1.5' + + //// Untested, but have aarch conda builds in bioconda/ conda-forge channels. + //// Should update the nf-core modules + + withName: 'BBSPLIT' { + conda = 'bioconda::bbmap=39.10' + // conda = 'bioconda::bbmap=39.01' + } + + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils=9.5' + //conda = 'conda-forge::coreutils=8.30' + } + + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'python=3.13.0' + //conda = 'conda-forge::coreutils=3.9.5' + } + + withName: 'FQ_SUBSAMPLE' { + conda = 'bioconda::fq=0.12.0' + //conda = 'bioconda::fq=0.9.1' } + + withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { + conda = 'bioconda::kallisto=0.51.1' + //conda = 'bioconda::kallisto=0.48.0' + } + + withName: 'PRESEQ_LCEXTRAP' { + conda = 'bioconda::preseq=3.2.0' + //conda = 'bioconda::preseq=3.1.2' + } + + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna=4.3.7' + //conda = 'bioconda::sortmerna=4.3.6' + } + + //// No longer necessary- dev branch version has an aarch 64 build (s) + + //withName: 'GUNZIP' { + // conda = 'conda-forge::sed' + // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + //} + + //withName: 'UNTAR' { + // conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' + // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + //} + + //withName: 'FASTP' { + // conda = 'bioconda::fastp' + // //conda = 'bioconda::fastp=0.23.4' + //} + + //withName: 'GFFREAD' { + // conda = 'bioconda::gffread' + // //conda = 'bioconda::gffread=0.12.7' + //} + + //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { + // conda = 'bioconda::umi_tools' + // //conda = 'bioconda::umi_tools=1.1.5' + //} + + //// No aarch64 builds in bioconda / conda-forge channels + + //// a) have seqera aarch64 conda builds - withName: 'UNTAR' { - conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' - //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + } + + withName: 'STAR_GENOMEGENERATE_IGENOMES' { + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' } -} + + withName: 'RSEM_PREPAREREFERENCE' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + } + + withName: 'RSEM_CALCULATEEXPRESSION' { + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + } + + // NOTE THE OLDER STAR VERSION HERE! + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } + + //// b) need aarch64 conda builds + + //withName: 'HISAT2_ALIGN' { + // conda = 'bioconda::hisat2 bioconda::samtools' + // //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' + //} + + //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { + // conda = 'bioconda::hisat2' + // //conda = 'bioconda::hisat2=2.2.1' + //} + +} From 328d02d1bd2c80c55743d804bc6e13db207fd66b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:32:03 +0100 Subject: [PATCH 18/82] Non-igenomes STAR can use the latest star --- conf/arm.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4a6f22e53..801473fa6 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -83,6 +83,11 @@ process { conda = 'bioconda::sortmerna=4.3.7' //conda = 'bioconda::sortmerna=4.3.6' } + + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } //// No longer necessary- dev branch version has an aarch 64 build (s) @@ -137,11 +142,6 @@ process { // NOTE THE OLDER STAR VERSION HERE! - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'seqera::star2.6.1d bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' - } - //// b) need aarch64 conda builds //withName: 'HISAT2_ALIGN' { From 2f92bfc2199e93ac8747128726130a09cb331544 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 18 Oct 2024 20:44:00 +0100 Subject: [PATCH 19/82] remove rogue comment --- conf/arm.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 801473fa6..55547a6fe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -140,8 +140,6 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' } - // NOTE THE OLDER STAR VERSION HERE! - //// b) need aarch64 conda builds //withName: 'HISAT2_ALIGN' { From 0a563dcedf654ac152ae04e8f4f10f97a5251335 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 11:58:41 +0100 Subject: [PATCH 20/82] update arm conf --- conf/arm.config | 73 ++++++++++++++++++------------------------------- 1 file changed, 26 insertions(+), 47 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 55547a6fe..4a56788fe 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -45,25 +45,12 @@ process { conda = 'bioconda::ucsc-bedgraphtobigwig=469' //conda = 'bioconda::ucsc-bedgraphtobigwig=445' } - - //// Untested, but have aarch conda builds in bioconda/ conda-forge channels. - //// Should update the nf-core modules - + withName: 'BBSPLIT' { conda = 'bioconda::bbmap=39.10' // conda = 'bioconda::bbmap=39.01' } - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils=9.5' - //conda = 'conda-forge::coreutils=8.30' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'python=3.13.0' - //conda = 'conda-forge::coreutils=3.9.5' - } - withName: 'FQ_SUBSAMPLE' { conda = 'bioconda::fq=0.12.0' //conda = 'bioconda::fq=0.9.1' @@ -73,48 +60,32 @@ process { conda = 'bioconda::kallisto=0.51.1' //conda = 'bioconda::kallisto=0.48.0' } - + withName: 'PRESEQ_LCEXTRAP' { conda = 'bioconda::preseq=3.2.0' //conda = 'bioconda::preseq=3.1.2' } - - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna=4.3.7' - //conda = 'bioconda::sortmerna=4.3.6' - } - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'seqera::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + withName: 'CAT_ADDITIONAL_FASTA' { + conda = 'python=3.13.0' + //conda = 'conda-forge::coreutils=3.9.5' } - //// No longer necessary- dev branch version has an aarch 64 build (s) - - //withName: 'GUNZIP' { - // conda = 'conda-forge::sed' - // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - //} - - //withName: 'UNTAR' { - // conda = 'conda-forge::grep conda-forge::sed conda-forge::tar' - // //conda = 'conda-forge::grep=3.11 conda-forge::sed=4.8 conda-forge::tar=1.34' - //} - - //withName: 'FASTP' { - // conda = 'bioconda::fastp' - // //conda = 'bioconda::fastp=0.23.4' - //} + //// Proposed to nf-core with Seqera container + + // Seqera container, since coreutils in existing image (ubuntu) wouldn't + // match update + withName: 'CAT_FASTQ' { + conda = 'conda-forge::coreutils=9.5' + //conda = 'conda-forge::coreutils=8.30' + } - //withName: 'GFFREAD' { - // conda = 'bioconda::gffread' - // //conda = 'bioconda::gffread=0.12.7' - //} + // Seqera container to avoid updating a mulled container - //withName: 'UMITOOLS_DEDUP|UMITOOLS_EXTRACT|UMITOOLS_PREPAREFORRSEM' { - // conda = 'bioconda::umi_tools' - // //conda = 'bioconda::umi_tools=1.1.5' - //} + withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { + conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' + //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' + } //// No aarch64 builds in bioconda / conda-forge channels @@ -152,4 +123,12 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} + //// c) have aarch64 builds in bioconda, but with problems + // sortmerna gives 'illegal instruction' errors at 5.3.7 with either + // Biocontainers or Seqera Containers + withName: 'SORTMERNA' { + conda = 'bioconda::sortmerna=4.3.7' + //conda = 'bioconda::sortmerna=4.3.6' + } + } From 8a3b58f4d2bdcb502d6961a253682c7c7f496c23 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 12:14:30 +0100 Subject: [PATCH 21/82] Bump lots of modules so that conda versions have arm builds --- modules.json | 118 +++---- modules/nf-core/bbmap/bbsplit/environment.yml | 2 +- modules/nf-core/bbmap/bbsplit/main.nf | 4 +- modules/nf-core/bbmap/bbsplit/meta.yml | 125 ++++--- .../bbmap/bbsplit/tests/main.nf.test.snap | 36 +- .../genomecov/bedtools-genomecov.diff | 37 -- modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/bedtools/genomecov/meta.yml | 72 ++-- .../bedtools/genomecov/tests/main.nf.test | 1 + .../nf-core/bracken/bracken/environment.yml | 2 - modules/nf-core/bracken/bracken/meta.yml | 75 ++-- .../bracken/bracken/tests/main.nf.test | 6 - modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/cat/fastq/main.nf | 4 +- modules/nf-core/cat/fastq/meta.yml | 43 +-- .../nf-core/cat/fastq/tests/main.nf.test.snap | 100 +++--- .../custom/catadditionalfasta/environment.yml | 2 +- .../nf-core/custom/catadditionalfasta/main.nf | 4 +- .../custom/catadditionalfasta/meta.yml | 89 ++--- .../catadditionalfasta/templates/fasta2gtf.py | 12 +- .../catadditionalfasta/tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 14 +- .../custom/getchromsizes/environment.yml | 5 +- modules/nf-core/custom/getchromsizes/main.nf | 4 +- modules/nf-core/custom/getchromsizes/meta.yml | 67 ++-- .../custom/getchromsizes/tests/main.nf.test | 1 + .../getchromsizes/tests/main.nf.test.snap | 40 +-- .../nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/custom/tx2gene/main.nf | 4 +- modules/nf-core/custom/tx2gene/meta.yml | 84 ++--- .../nf-core/custom/tx2gene/tests/main.nf.test | 1 + .../custom/tx2gene/tests/main.nf.test.snap | 20 +- modules/nf-core/dupradar/meta.yml | 147 +++++--- modules/nf-core/dupradar/tests/main.nf.test | 1 + modules/nf-core/fastp/meta.yml | 138 +++++--- modules/nf-core/fq/subsample/environment.yml | 2 +- modules/nf-core/fq/subsample/main.nf | 4 +- modules/nf-core/fq/subsample/meta.yml | 48 +-- .../nf-core/fq/subsample/tests/main.nf.test | 1 + .../fq/subsample/tests/main.nf.test.snap | 195 ++--------- modules/nf-core/gffread/meta.yml | 84 +++-- modules/nf-core/gffread/tests/main.nf.test | 1 + modules/nf-core/gunzip/meta.yml | 37 +- .../nf-core/hisat2/align/hisat2-align.diff | 22 +- modules/nf-core/hisat2/align/meta.yml | 107 +++--- modules/nf-core/hisat2/build/meta.yml | 83 ++--- .../hisat2/extractsplicesites/meta.yml | 49 +-- .../nf-core/kallisto/index/environment.yml | 2 +- modules/nf-core/kallisto/index/main.nf | 4 +- modules/nf-core/kallisto/index/meta.yml | 47 +-- .../nf-core/kallisto/index/tests/main.nf.test | 3 +- .../kallisto/index/tests/main.nf.test.snap | 43 +-- .../nf-core/kallisto/quant/environment.yml | 2 +- modules/nf-core/kallisto/quant/main.nf | 4 +- modules/nf-core/kallisto/quant/meta.yml | 128 ++++--- .../kallisto/quant/tests/main.nf.test.snap | 40 +-- .../nf-core/kraken2/kraken2/environment.yml | 2 - modules/nf-core/kraken2/kraken2/meta.yml | 121 ++++--- .../kraken2/kraken2/tests/main.nf.test | 5 - .../nf-core/preseq/lcextrap/environment.yml | 2 +- modules/nf-core/preseq/lcextrap/main.nf | 4 +- modules/nf-core/preseq/lcextrap/meta.yml | 63 ++-- .../preseq/lcextrap/tests/main.nf.test.snap | 36 +- modules/nf-core/qualimap/rnaseq/meta.yml | 61 ++-- .../nf-core/rsem/calculateexpression/meta.yml | 120 +++++-- .../nf-core/rsem/preparereference/meta.yml | 40 ++- modules/nf-core/rseqc/bamstat/meta.yml | 37 +- .../nf-core/rseqc/bamstat/tests/main.nf.test | 2 + .../nf-core/rseqc/inferexperiment/meta.yml | 45 ++- .../rseqc/inferexperiment/tests/main.nf.test | 1 + modules/nf-core/rseqc/innerdistance/meta.yml | 89 +++-- .../rseqc/innerdistance/tests/main.nf.test | 1 + .../nf-core/rseqc/junctionannotation/meta.yml | 117 ++++--- .../junctionannotation/tests/main.nf.test | 1 + .../nf-core/rseqc/junctionsaturation/meta.yml | 56 +-- .../junctionsaturation/tests/main.nf.test | 1 + .../nf-core/rseqc/readdistribution/meta.yml | 45 ++- .../nf-core/rseqc/readduplication/meta.yml | 74 ++-- modules/nf-core/rseqc/tin/meta.yml | 64 ++-- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/index/main.nf | 4 +- modules/nf-core/salmon/index/meta.yml | 27 +- .../salmon/index/tests/main.nf.test.snap | 16 +- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/salmon/quant/main.nf | 4 +- modules/nf-core/salmon/quant/meta.yml | 94 +++-- .../salmon/quant/tests/main.nf.test.snap | 64 ++-- .../nf-core/samtools/flagstat/environment.yml | 6 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- modules/nf-core/samtools/flagstat/meta.yml | 54 +-- .../samtools/flagstat/tests/main.nf.test.snap | 16 +- .../nf-core/samtools/idxstats/environment.yml | 6 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- modules/nf-core/samtools/idxstats/meta.yml | 51 +-- .../samtools/idxstats/tests/main.nf.test.snap | 16 +- .../nf-core/samtools/index/environment.yml | 6 +- modules/nf-core/samtools/index/main.nf | 4 +- modules/nf-core/samtools/index/meta.yml | 68 ++-- .../samtools/index/tests/main.nf.test.snap | 46 +-- modules/nf-core/samtools/sort/environment.yml | 6 +- modules/nf-core/samtools/sort/main.nf | 15 +- modules/nf-core/samtools/sort/meta.yml | 99 +++--- .../nf-core/samtools/sort/tests/main.nf.test | 64 ++++ .../samtools/sort/tests/main.nf.test.snap | 125 ++++++- .../nf-core/samtools/stats/environment.yml | 6 +- modules/nf-core/samtools/stats/main.nf | 4 +- modules/nf-core/samtools/stats/meta.yml | 69 ++-- .../nf-core/samtools/stats/tests/main.nf.test | 1 + .../samtools/stats/tests/main.nf.test.snap | 40 +-- modules/nf-core/sortmerna/meta.yml | 121 ++++--- modules/nf-core/sortmerna/tests/main.nf.test | 2 +- modules/nf-core/star/align/environment.yml | 5 +- modules/nf-core/star/align/main.nf | 33 +- modules/nf-core/star/align/meta.yml | 269 ++++++++++----- .../star/align/tests/main.nf.test.snap | 324 ++++++++++-------- .../star/align/tests/nextflow.arriba.config | 3 - .../nf-core/star/align/tests/nextflow.config | 3 - .../align/tests/nextflow.starfusion.config | 3 - .../star/genomegenerate/environment.yml | 3 +- modules/nf-core/star/genomegenerate/meta.yml | 57 +-- .../stringtie/stringtie/environment.yml | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 4 +- modules/nf-core/stringtie/stringtie/meta.yml | 89 +++-- .../stringtie/tests/main.nf.test.snap | 64 ++-- .../subread/featurecounts/environment.yml | 2 +- modules/nf-core/subread/featurecounts/main.nf | 4 +- .../nf-core/subread/featurecounts/meta.yml | 68 ++-- .../featurecounts/tests/main.nf.test.snap | 78 ++--- .../summarizedexperiment/meta.yml | 112 +++--- .../summarizedexperiment/tests/main.nf.test | 1 + modules/nf-core/trimgalore/environment.yml | 4 +- modules/nf-core/trimgalore/main.nf | 4 +- .../trimgalore/tests/main.nf.test.snap | 36 +- modules/nf-core/tximeta/tximport/meta.yml | 198 ++++++----- .../tximeta/tximport/tests/main.nf.test | 1 + modules/nf-core/ucsc/bedclip/meta.yml | 48 +-- .../ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 8 +- .../nf-core/ucsc/bedgraphtobigwig/meta.yml | 53 +-- .../bedgraphtobigwig/tests/main.nf.test.snap | 16 +- modules/nf-core/umitools/dedup/meta.yml | 118 ++++--- .../nf-core/umitools/dedup/tests/main.nf.test | 1 + .../nf-core/umitools/prepareforrsem/meta.yml | 70 ++-- .../prepareforrsem/tests/main.nf.test | 1 + modules/nf-core/untar/meta.yml | 43 +-- .../tests/main.nf.test.snap | 42 +-- .../tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 86 ++--- .../tests/main.nf.test.snap | 80 ++--- .../tests/main.nf.test.snap | 96 +++--- .../tests/main.nf.test.snap | 20 +- .../fastq_align_hisat2/tests/main.nf.test | 3 + .../tests/main.nf.test.snap | 84 ++--- .../tests/main.nf.test | 2 + .../tests/main.nf.test.snap | 44 +-- .../tests/main.nf.test.snap | 24 +- .../tests/main.nf.test | 2 + .../tests/main.nf.test.snap | 48 +-- .../utils_nfschema_plugin/tests/main.nf.test | 4 - 159 files changed, 3633 insertions(+), 2834 deletions(-) delete mode 100644 modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff diff --git a/modules.json b/modules.json index 6a263bfc8..c64fdaea8 100644 --- a/modules.json +++ b/modules.json @@ -7,48 +7,48 @@ "nf-core": { "bbmap/bbsplit": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "bedtools/genomecov": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", "installed_by": ["modules"], "patch": "modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff" }, "bracken/bracken": { "branch": "master", - "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "custom/catadditionalfasta": { "branch": "master", - "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", - "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "dupradar": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { @@ -58,48 +58,48 @@ }, "fq/subsample": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_subsample_fq_salmon", "modules"] }, "gffread": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", - "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_align_hisat2"], "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", - "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "kallisto/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "kallisto/quant": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "kraken2/kraken2": { "branch": "master", - "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { @@ -115,87 +115,87 @@ }, "preseq/lcextrap": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rsem/calculateexpression": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rsem/preparereference": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rseqc/bamstat": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/inferexperiment": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/innerdistance": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/junctionannotation": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/junctionsaturation": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/readdistribution": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/readduplication": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "rseqc/tin": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_rseqc"] }, "salmon/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["fastq_subsample_fq_salmon"] }, "salmon/quant": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": [ "bam_dedup_stats_samtools_umitools", "bam_markduplicates_picard", @@ -204,67 +204,67 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["bam_stats_samtools"] }, "sortmerna": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "star/align": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "summarizedexperiment/summarizedexperiment": { "branch": "master", - "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "trimgalore": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { "branch": "master", - "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "ucsc/bedclip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "ucsc/bedgraphtobigwig": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "umitools/dedup": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["bam_dedup_stats_samtools_umitools"] }, "umitools/extract": { @@ -274,12 +274,12 @@ }, "umitools/prepareforrsem": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -288,12 +288,12 @@ "nf-core": { "bam_dedup_stats_samtools_umitools": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["subworkflows"] }, "bam_markduplicates_picard": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["subworkflows"] }, "bam_rseqc": { @@ -303,12 +303,12 @@ }, "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["fastq_align_hisat2"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": [ "bam_dedup_stats_samtools_umitools", "bam_markduplicates_picard", @@ -317,12 +317,12 @@ }, "bedgraph_bedclip_bedgraphtobigwig": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["subworkflows"] }, "fastq_align_hisat2": { "branch": "master", - "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["subworkflows"] }, "fastq_fastqc_umitools_fastp": { @@ -332,7 +332,7 @@ }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", - "git_sha": "4026bab16a91b1b0b18d80ff465819ca725f33fd", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { @@ -342,12 +342,12 @@ }, "fastq_subsample_fq_salmon": { "branch": "master", - "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "quantify_pseudo_alignment": { "branch": "master", - "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index dfd8936e1..a2f655067 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bbmap=39.01 + - bioconda::bbmap=39.10 diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf index f308f6983..9eb53208c 100644 --- a/modules/nf-core/bbmap/bbsplit/main.nf +++ b/modules/nf-core/bbmap/bbsplit/main.nf @@ -5,8 +5,8 @@ process BBMAP_BBSPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0': - 'biocontainers/bbmap:39.01--h5c4e2a8_0' }" + 'https://depot.galaxyproject.org/singularity/bbmap:39.10--h92535d8_0': + 'biocontainers/bbmap:39.10--h92535d8_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml index f4e0a5ed5..c34196e47 100644 --- a/modules/nf-core/bbmap/bbsplit/meta.yml +++ b/modules/nf-core/bbmap/bbsplit/meta.yml @@ -8,64 +8,91 @@ keywords: - reference tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Directory to place generated index - pattern: "*" - - primary_ref: - type: file - description: Path to the primary reference - pattern: "*" - - other_ref_names: - type: list - description: List of other reference ids apart from the primary - - other_ref_paths: - type: list - description: Path to other references paths corresponding to "other_ref_names" - - only_build_index: - type: string - description: true = only build index; false = mapping + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Directory to place generated index + pattern: "*" + - - primary_ref: + type: file + description: Path to the primary reference + pattern: "*" + - - other_ref_names: + type: list + description: List of other reference ids apart from the primary + - other_ref_paths: + type: list + description: Path to other references paths corresponding to "other_ref_names" + - - only_build_index: + type: string + description: true = only build index; false = mapping output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Directory with index files - pattern: "bbsplit" + - bbsplit: + type: directory + description: Directory with index files + pattern: "bbsplit" - primary_fastq: - type: file - description: Output reads that map to the primary reference - pattern: "*primary*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*primary*fastq.gz": + type: file + description: Output reads that map to the primary reference + pattern: "*primary*fastq.gz" - all_fastq: - type: file - description: All reads mapping to any of the references - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: All reads mapping to any of the references + pattern: "*fastq.gz" - stats: - type: file - description: Tab-delimited text file containing mapping statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*txt": + type: file + description: Tab-delimited text file containing mapping statistics + pattern: "*.txt" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap index 0d648d7d6..6bdc3c0d1 100644 --- a/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/bbsplit/tests/main.nf.test.snap @@ -9,26 +9,26 @@ "namelist.txt:md5,45e7a4cdc7a11a39ada56844ca3a1e30" ], [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:41:32.116928" + "timestamp": "2024-10-19T16:03:51.869574777" }, "sarscov2_se_fastq_fasta_chr22_fasta - index": { "content": [ [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:41:06.072212" + "timestamp": "2024-10-19T15:47:22.996403051" }, "sarscov2_se_fastq_fasta_chr22_fasta - index - stub": { "content": [ @@ -56,7 +56,7 @@ ] ], "5": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ], "all_fastq": [ @@ -81,15 +81,15 @@ ], "versions": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:45:21.48352" + "timestamp": "2024-10-19T16:03:10.27746726" }, "sarscov2_se_fastq_fasta_chr22_fasta - stub": { "content": [ @@ -139,7 +139,7 @@ ] ], "5": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ], "all_fastq": [ [ @@ -186,14 +186,14 @@ ] ], "versions": [ - "versions.yml:md5,cb7f0e697ab2537f8ced951bfade90d4" + "versions.yml:md5,97dfea8bc38fdb0ec800ee936e0c6e27" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T11:51:38.805111" + "timestamp": "2024-10-19T16:04:18.416324262" } } \ No newline at end of file diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff deleted file mode 100644 index 53d7e34df..000000000 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ /dev/null @@ -1,37 +0,0 @@ -Changes in module 'nf-core/bedtools/genomecov' -Changes in 'bedtools/genomecov/main.nf': ---- modules/nf-core/bedtools/genomecov/main.nf -+++ modules/nf-core/bedtools/genomecov/main.nf -@@ -4,8 +4,8 @@ - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': -- 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': -+ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" - - input: - tuple val(meta), path(intervals), val(scale) - -'modules/nf-core/bedtools/genomecov/meta.yml' is unchanged -'modules/nf-core/bedtools/genomecov/environment.yml' is unchanged -'modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap' is unchanged -'modules/nf-core/bedtools/genomecov/tests/nextflow.config' is unchanged -Changes in 'bedtools/genomecov/tests/main.nf.test': ---- modules/nf-core/bedtools/genomecov/tests/main.nf.test -+++ modules/nf-core/bedtools/genomecov/tests/main.nf.test -@@ -3,11 +3,6 @@ - script "../main.nf" - process "BEDTOOLS_GENOMECOV" - config "./nextflow.config" -- -- tag "modules" -- tag "modules_nfcore" -- tag "bedtools" -- tag "bedtools/genomecov" - - test("sarscov2 - no scale") { - when { - -************************************************************ diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 91869ec23..35e2ab14b 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_GENOMECOV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" + 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml index 2b2385e3e..41b1f8f49 100644 --- a/modules/nf-core/bedtools/genomecov/meta.yml +++ b/modules/nf-core/bedtools/genomecov/meta.yml @@ -1,5 +1,6 @@ name: bedtools_genomecov -description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. +description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) + summaries of feature coverage (e.g., aligned sequences) for a given genome. keywords: - bed - bam @@ -12,39 +13,50 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - scale: - type: integer - description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - - sizes: - type: file - description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - scale: + type: integer + description: Number containing the scale factor for the output. Set to 1 to + disable. Setting to a value other than 1 will also get the -bg bedgraph output + format as this is required for this command switch + - - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and + chromosome sizes in the second column + - - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", + ".tab", etc.) It is set arbitrarily by the user and corresponds to the file + format which depends on arguments. + - - sort: + type: boolean + description: Sort the output output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - genomecov: - type: file - description: Computed genome coverage file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Computed genome coverage file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test index b8caa1e11..13f043102 100644 --- a/modules/nf-core/bedtools/genomecov/tests/main.nf.test +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { process "BEDTOOLS_GENOMECOV" config "./nextflow.config" + test("sarscov2 - no scale") { when { process { diff --git a/modules/nf-core/bracken/bracken/environment.yml b/modules/nf-core/bracken/bracken/environment.yml index 6eb5b1b9a..b96b00d7a 100644 --- a/modules/nf-core/bracken/bracken/environment.yml +++ b/modules/nf-core/bracken/bracken/environment.yml @@ -1,7 +1,5 @@ -name: bracken_bracken channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bracken=2.9" diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml index b7ff4489f..85a267efc 100644 --- a/modules/nf-core/bracken/bracken/meta.yml +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -7,44 +7,61 @@ keywords: - kraken2 tools: - bracken: - description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. homepage: https://ccb.jhu.edu/software/bracken/ documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual tool_dev_url: https://github.com/jenniferlu717/Bracken doi: "10.7717/peerj-cs.104" licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kraken_report: - type: file - description: TSV file with six columns coming from kraken2 output - pattern: "*.{tsv}" - - database: - type: file - description: Directory containing the kraken2/Bracken files for analysis - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_report: + type: file + description: TSV file with six columns coming from kraken2 output + pattern: "*.{tsv}" + - - database: + type: file + description: Directory containing the kraken2/Bracken files for analysis + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reports: - type: file - description: TSV output report of the re-estimated abundances - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" + - bracken_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" - txt: - type: file - description: TXT file of bracken corrected results of Kraken2 report output - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - bracken_kraken_style_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/bracken/bracken/tests/main.nf.test b/modules/nf-core/bracken/bracken/tests/main.nf.test index 9d2105ded..3085f3f89 100644 --- a/modules/nf-core/bracken/bracken/tests/main.nf.test +++ b/modules/nf-core/bracken/bracken/tests/main.nf.test @@ -4,12 +4,6 @@ nextflow_process { script "../main.nf" process "BRACKEN_BRACKEN" - tag "modules" - tag "modules_nfcore" - tag "bracken" - tag "bracken/bracken" - tag "kraken2/kraken2" - tag "untar" setup { run ("UNTAR") { diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index c7eb9bd1c..71e04c3d7 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index b68e5f911..4364a389b 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -4,8 +4,8 @@ process CAT_FASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index db4ac3c79..91ff2fb5f 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,30 +10,33 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index aec119a94..f8689a1ce 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:30:39.816981" + "timestamp": "2024-10-19T20:02:07.519211144" }, "test_cat_fastq_single_end_same_name": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:35.229332" + "timestamp": "2024-10-19T20:02:31.618628921" }, "test_cat_fastq_single_end_single_file": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:34:00.058829" + "timestamp": "2024-10-19T20:02:57.904149581" }, "test_cat_fastq_paired_end_same_name": { "content": [ @@ -120,7 +120,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -135,15 +135,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:33:33.031555" + "timestamp": "2024-10-19T20:02:44.577183829" }, "test_cat_fastq_single_end - stub": { "content": [ @@ -158,7 +158,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -170,15 +170,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:28.244999" + "timestamp": "2024-10-19T20:03:10.603734777" }, "test_cat_fastq_paired_end_same_name - stub": { "content": [ @@ -196,7 +196,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -211,15 +211,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:57.070911" + "timestamp": "2024-10-19T20:03:46.041808828" }, "test_cat_fastq_single_end_same_name - stub": { "content": [ @@ -234,7 +234,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -246,15 +246,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:46.796254" + "timestamp": "2024-10-19T20:03:34.13865402" }, "test_cat_fastq_paired_end": { "content": [ @@ -272,7 +272,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -287,15 +287,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:32:02.270935" + "timestamp": "2024-10-19T20:02:19.64383573" }, "test_cat_fastq_paired_end - stub": { "content": [ @@ -313,7 +313,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -328,15 +328,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:07:37.807553" + "timestamp": "2024-10-19T20:03:22.597246066" }, "test_cat_fastq_single_end_single_file - stub": { "content": [ @@ -351,7 +351,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -363,14 +363,14 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:14:51.861264" + "timestamp": "2024-10-19T20:03:58.44849001" } } \ No newline at end of file diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index 1d80d11a9..2000006c4 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::python=3.9.5 + - conda-forge::python=3.12.2 diff --git a/modules/nf-core/custom/catadditionalfasta/main.nf b/modules/nf-core/custom/catadditionalfasta/main.nf index 88ce4954b..9925ca322 100644 --- a/modules/nf-core/custom/catadditionalfasta/main.nf +++ b/modules/nf-core/custom/catadditionalfasta/main.nf @@ -3,8 +3,8 @@ process CUSTOM_CATADDITIONALFASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" + 'https://depot.galaxyproject.org/singularity/python:3.12' : + 'biocontainers/python:3.12' }" input: tuple val(meta), path(fasta), path(gtf) diff --git a/modules/nf-core/custom/catadditionalfasta/meta.yml b/modules/nf-core/custom/catadditionalfasta/meta.yml index 8a9505d30..e6c313d39 100644 --- a/modules/nf-core/custom/catadditionalfasta/meta.yml +++ b/modules/nf-core/custom/catadditionalfasta/meta.yml @@ -1,60 +1,67 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_catadditionalfasta" -description: Custom module to Add a new fasta file to an old one and update an associated GTF +description: Custom module to Add a new fasta file to an old one and update an associated + GTF keywords: - fasta - gtf - genomics tools: - "custom": - description: "Custom module to Add a new fasta file to an old one and update an associated GTF" + description: "Custom module to Add a new fasta file to an old one and update an + associated GTF" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing fasta information - - meta2: - type: map - description: | - Groovy Map containing additional fasta information - - fasta: - type: file - description: FASTA-format sequence file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: GTF-format annotation file for fasta - pattern: "*.gtf" - - add_fasta: - type: file - description: FASTA-format file of additional sequences - pattern: "*.fa" - - biotype: - type: string - description: Biotype to apply to new GTF entries - + - - meta: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: FASTA-format sequence file + pattern: "*.{fasta,fa}" + - gtf: + type: file + description: GTF-format annotation file for fasta + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing additional fasta information + - add_fasta: + type: file + description: FASTA-format file of additional sequences + pattern: "*.fa" + - - biotype: + type: string + description: Biotype to apply to new GTF entries output: - - meta: - type: map - description: | - Groovy Map containing fasta information - fasta: - type: file - description: FASTA-format combined sequence file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.fasta": + type: file + description: FASTA-format combined sequence file + pattern: "*.{fasta,fa}" - gtf: - type: file - description: GTF-format combined annotation file - pattern: "*.gtf" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.gtf": + type: file + description: GTF-format combined annotation file + pattern: "*.gtf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py index 06b4c253a..c7351e568 100755 --- a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py +++ b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py @@ -114,16 +114,8 @@ def main() -> None: fasta_to_gtf("$add_fasta", f"{add_name}.gtf", "$biotype") # Concatenate new fasta to existing fasta, and the GTF we just generated to the GTF - genome_name = ( - "$params.genome" - if "$params.genome" != "null" - else os.path.splitext(os.path.basename("$fasta"))[0] - ) - output_prefix = ( - "$task.ext.prefix" - if "$task.ext.prefix" != "null" - else f"{genome_name}_{add_name}" - ) + genome_name = "$params.genome" if "$params.genome" != "null" else os.path.splitext(os.path.basename("$fasta"))[0] + output_prefix = "$task.ext.prefix" if "$task.ext.prefix" != "null" else f"{genome_name}_{add_name}" os.mkdir("out") os.system(f"cat $fasta $add_fasta > out/{output_prefix}.fasta") diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test index 878c05d16..f13f39fa4 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "CUSTOM_CATADDITIONALFASTA" + test("sarscov2 - fastq - gtf") { when { diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap index 4767fd9a0..6dd1afeb1 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,26f47339777a265af57338ac7f0f8798" + "versions.yml:md5,5917ae30ad1ee71ad6b62659d5b628d1" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:19:28.965471" + "timestamp": "2024-10-19T21:07:02.01253345" }, "sarscov2 - fastq - gtf - stub": { "content": [ @@ -77,9 +77,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:19:38.549677" + "timestamp": "2024-10-19T21:07:12.9817063" } } \ No newline at end of file diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index da2df5e43..2bcd47ee1 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 3edf7c221..d8c7405c6 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml index 529be07e4..2a0e8da0a 100644 --- a/modules/nf-core/custom/getchromsizes/meta.yml +++ b/modules/nf-core/custom/getchromsizes/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna,fas}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna,fas}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sizes: - type: file - description: File containing chromosome lengths - pattern: "*.{sizes}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: File containing chromosome lengths + pattern: "*.{sizes}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test index 2dadc1a55..8a05aeaae 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "CUSTOM_GETCHROMSIZES" + test("test_custom_getchromsizes") { when { diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap index c37b284d7..d2072e22c 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:38:36.927106" + "timestamp": "2024-10-18T10:11:37.459094476" }, "test_custom_getchromsizes": { "content": [ @@ -87,7 +87,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -109,15 +109,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:22:34.14237" + "timestamp": "2024-10-18T10:11:01.526301351" }, "test_custom_getchromsizes_bgzip": { "content": [ @@ -147,7 +147,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -174,15 +174,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:23:06.241379" + "timestamp": "2024-10-18T10:11:14.32456385" }, "test_custom_getchromsizes - stub": { "content": [ @@ -207,7 +207,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -229,14 +229,14 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:24:05.697845" + "timestamp": "2024-10-18T10:11:26.505487624" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index 9f5f9fb9b..9824d0c27 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python=3.9.5 + - python=3.10.4 diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf index 99c00aa06..eed5e97b1 100644 --- a/modules/nf-core/custom/tx2gene/main.nf +++ b/modules/nf-core/custom/tx2gene/main.nf @@ -4,8 +4,8 @@ process CUSTOM_TX2GENE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" + 'https://depot.galaxyproject.org/singularity/python:3.10.4' : + 'biocontainers/python:3.10.4' }" input: tuple val(meta), path(gtf) diff --git a/modules/nf-core/custom/tx2gene/meta.yml b/modules/nf-core/custom/tx2gene/meta.yml index d991bf1be..8254afa08 100644 --- a/modules/nf-core/custom/tx2gene/meta.yml +++ b/modules/nf-core/custom/tx2gene/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_tx2gene" -description: Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. +description: Make a transcript/gene mapping from a GTF and cross-reference with transcript + quantifications. keywords: - gene - gtf @@ -14,51 +14,51 @@ tools: check it against transcript quantifications" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" - - meta2: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - - id: - type: string - description: Gene ID attribute in the GTF file (default= gene_id) - - extra: - type: string - description: Extra gene attribute in the GTF file (default= gene_name) - + - - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: file + description: quants file + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' + - - id: + type: string + description: Gene ID attribute in the GTF file (default= gene_id) + - - extra: + type: string + description: Extra gene attribute in the GTF file (default= gene_name) output: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - tx2gene: - type: file - description: A transcript/ gene mapping table in TSV format - pattern: "*.tx2gene.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - "*tx2gene.tsv": + type: file + description: A transcript/ gene mapping table in TSV format + pattern: "*.tx2gene.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index e56a0b8fe..2d45b7646 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "CUSTOM_TX2GENE" + test("saccharomyces_cerevisiae - gtf") { setup { diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index c19f10f71..2be5fe547 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ], "tx2gene": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:13:11.305047" + "timestamp": "2024-10-18T10:24:12.19104487" }, "saccharomyces_cerevisiae - gtf - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ], "tx2gene": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T15:15:34.064489" + "timestamp": "2024-10-18T10:24:24.729694098" } } \ No newline at end of file diff --git a/modules/nf-core/dupradar/meta.yml b/modules/nf-core/dupradar/meta.yml index 95960ae98..a532519fe 100644 --- a/modules/nf-core/dupradar/meta.yml +++ b/modules/nf-core/dupradar/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "dupradar" description: Assessment of duplication rates in RNA-Seq datasets @@ -14,71 +13,109 @@ tools: tool_dev_url: "https://github.com/ssayols/dupRadar" doi: "10.1186/s12859-016-1276-2" licence: ["GPL v3"] + identifier: biotools:dupradar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'human' ] - - gtf: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file containing read alignments + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'human' ] + - gtf: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - scatter2d: - type: file - description: PDF duplication rate against total read count plot - pattern: "*_duprateExpDens.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpDens.pdf": + type: file + description: PDF duplication rate against total read count plot + pattern: "*_duprateExpDens.pdf" - boxplot: - type: file - description: | - PDF duplication rate ~ total reads per kilobase (RPK) boxplot - pattern: "*_duprateExpBoxplot.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpBoxplot.pdf": + type: file + description: | + PDF duplication rate ~ total reads per kilobase (RPK) boxplot + pattern: "*_duprateExpBoxplot.pdf" - hist: - type: file - description: | - PDF expression histogram - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_expressionHist.pdf": + type: file + description: | + PDF expression histogram + pattern: "*.pdf" - dupmatrix: - type: file - description: | - Text file containing tags falling on the features described in the GTF - file - pattern: "*_dupMatrix.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_dupMatrix.txt": + type: file + description: | + Text file containing tags falling on the features described in the GTF + file + pattern: "*_dupMatrix.txt" - intercept_slope: - type: file - description: | - Text file containing intercept and slope from dupRadar modelling - pattern: "*_intercept_slope.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_intercept_slope.txt": + type: file + description: | + Text file containing intercept and slope from dupRadar modelling + pattern: "*_intercept_slope.txt" - multiqc: - type: file - description: | - dupRadar files for passing to MultiQC - pattern: "*_multiqc.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_mqc.txt": + type: file + description: | + dupRadar files for passing to MultiQC + pattern: "*_multiqc.txt" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/dupradar/tests/main.nf.test b/modules/nf-core/dupradar/tests/main.nf.test index 60f8dfb7d..d45cefcfe 100644 --- a/modules/nf-core/dupradar/tests/main.nf.test +++ b/modules/nf-core/dupradar/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "DUPRADAR" + test("sarscov2 - bam - single_end") { config './nextflow.config' diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 8dfecc184..159404d08 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -11,66 +11,100 @@ tools: documentation: https://github.com/OpenGene/fastp doi: 10.1093/bioinformatics/bty560 licence: ["MIT"] + identifier: biotools:fastp input: - - meta: - type: map - description: | - Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. If you wish to run interleaved paired-end data, supply as single-end data - but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. | - This can be used to use fastp for the output report only. - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + - - meta: + type: map + description: | + Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. If you wish to run interleaved paired-end data, supply as single-end data + but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. + - - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + - - discard_trimmed_pass: + type: boolean + description: Specify true to not write any reads that pass trimming thresholds. + | This can be used to use fastp for the output report only. + - - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified/unmerged fastq reads - pattern: "*fastp.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastp.fastq.gz": + type: file + description: The trimmed/modified/unmerged fastq reads + pattern: "*fastp.fastq.gz" - json: - type: file - description: Results in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.json" - html: - type: file - description: Results in HTML format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format + pattern: "*.html" - log: - type: file - description: fastq log file - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" - reads_fail: - type: file - description: Reads the failed the preprocessing - pattern: "*fail.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fail.fastq.gz": + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" - reads_merged: - type: file - description: Reads that were successfully merged - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Reads that were successfully merged + pattern: "*.{merged.fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index eaba9339b..74b146083 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::fq=0.9.1 + - bioconda::fq=0.12.0 diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf index a8e647bb1..d66f0cd1a 100644 --- a/modules/nf-core/fq/subsample/main.nf +++ b/modules/nf-core/fq/subsample/main.nf @@ -4,8 +4,8 @@ process FQ_SUBSAMPLE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0': - 'biocontainers/fq:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/fq:0.12.0--h9ee0642_0': + 'biocontainers/fq:0.12.0--h9ee0642_0' }" input: tuple val(meta), path(fastq) diff --git a/modules/nf-core/fq/subsample/meta.yml b/modules/nf-core/fq/subsample/meta.yml index 6c5e87f3e..7d91b0d9a 100644 --- a/modules/nf-core/fq/subsample/meta.yml +++ b/modules/nf-core/fq/subsample/meta.yml @@ -1,5 +1,6 @@ name: "fq_subsample" -description: fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args. +description: fq subsample outputs a subset of records from single or paired FASTQ + files. This requires a seed (--seed) to be set in ext.args. keywords: - fastq - fq @@ -11,30 +12,33 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file - pattern: "*.{fq,fastq}{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file + pattern: "*.{fq,fastq}{,.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Randomly sampled FASTQ files. - pattern: "*_R[12].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Randomly sampled FASTQ files. + pattern: "*_R[12].fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test b/modules/nf-core/fq/subsample/tests/main.nf.test index 13bb75945..a7880501b 100644 --- a/modules/nf-core/fq/subsample/tests/main.nf.test +++ b/modules/nf-core/fq/subsample/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "FQ_SUBSAMPLE" + test("test_fq_subsample_no_args") { config "./nextflow_no_args.config" when { diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test.snap b/modules/nf-core/fq/subsample/tests/main.nf.test.snap index 739c626d7..cf0b0f254 100644 --- a/modules/nf-core/fq/subsample/tests/main.nf.test.snap +++ b/modules/nf-core/fq/subsample/tests/main.nf.test.snap @@ -15,7 +15,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -30,15 +30,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T08:26:12.163153" + "timestamp": "2024-10-19T16:33:49.881713827" }, "test_fq_subsample_probability": { "content": [ @@ -56,7 +56,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -71,15 +71,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:57:15.446336" + "timestamp": "2024-10-19T16:33:38.284916869" }, "test_fq_subsample_single - stub": { "content": [ @@ -97,7 +97,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -112,56 +112,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T08:26:55.736374" - }, - "test_fq_subsample_no_args - sub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T08:25:42.190405" + "timestamp": "2024-10-19T16:34:47.477222088" }, "test_fq_subsample_record_count": { "content": [ @@ -179,7 +138,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -194,56 +153,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:57:23.920058" - }, - "stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T17:16:10.090213" + "timestamp": "2024-10-19T16:34:02.461958921" }, "test_fq_subsample_single": { "content": [ @@ -258,7 +176,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -270,15 +188,15 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-17T17:57:31.908993" + "timestamp": "2024-10-19T16:34:27.295010129" }, "test_fq_subsample_no_args": { "content": [ @@ -298,10 +216,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-10-17T11:17:09.761156" + "timestamp": "2024-10-19T16:33:26.427718685" }, "test_fq_subsample_no_input": { "content": [ @@ -321,10 +239,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-10-17T11:17:37.555824" + "timestamp": "2024-10-19T16:35:00.624040224" }, "test_fq_subsample_record_count - stub": { "content": [ @@ -342,48 +260,7 @@ ] ], "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T08:26:33.873553" - }, - "test_fq_subsample_no_input - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ], "fastq": [ [ @@ -398,14 +275,14 @@ ] ], "versions": [ - "versions.yml:md5,ffbf935bd0de512fbc9e83b187bf924f" + "versions.yml:md5,cd1dcdb5fdaf7a8318f83f7f7f9082a1" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T08:27:21.793136" + "timestamp": "2024-10-19T16:34:14.613246906" } } \ No newline at end of file diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index c06028208..bebe7f575 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -1,53 +1,73 @@ name: gffread -description: Validate, filter, convert and perform various other operations on GFF files +description: Validate, filter, convert and perform various other operations on GFF + files keywords: - gff - conversion - validation tools: - gffread: - description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more. + description: GFF/GTF utility providing format conversions, region filtering, FASTA + sequence extraction and more. homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] + identifier: biotools:gffread input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - gff: + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" + - - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - gtf: - type: file - description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present - pattern: "*.{gtf}" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gtf": + type: file + description: GTF file resulting from the conversion of the GFF input file if + '-T' argument is present + pattern: "*.{gtf}" - gffread_gff: - type: file - description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gff3": + type: file + description: GFF3 file resulting from the conversion of the GFF input file if + '-T' argument is absent + pattern: "*.gff3" - gffread_fasta: - type: file - description: Fasta file produced when either of '-w', '-x', '-y' parameters is present - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.fasta": + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters + is present + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index e03820f4d..6d7c063ef 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "GFFREAD" + test("sarscov2-gff3-gtf") { config "./nextflow.config" diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a0a..9066c0353 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/hisat2/align/hisat2-align.diff b/modules/nf-core/hisat2/align/hisat2-align.diff index 2a64e4f4f..216a70049 100644 --- a/modules/nf-core/hisat2/align/hisat2-align.diff +++ b/modules/nf-core/hisat2/align/hisat2-align.diff @@ -1,4 +1,7 @@ Changes in module 'nf-core/hisat2/align' +'modules/nf-core/hisat2/align/environment.yml' is unchanged +'modules/nf-core/hisat2/align/meta.yml' is unchanged +Changes in 'hisat2/align/main.nf': --- modules/nf-core/hisat2/align/main.nf +++ modules/nf-core/hisat2/align/main.nf @@ -34,7 +34,7 @@ @@ -30,6 +33,17 @@ Changes in module 'nf-core/hisat2/align' ${unaligned} +'modules/nf-core/hisat2/align/tests/main.nf.test.snap' is unchanged +Changes in 'hisat2/align/tests/tags.yml': +--- modules/nf-core/hisat2/align/tests/tags.yml ++++ modules/nf-core/hisat2/align/tests/tags.yml +@@ -1,4 +0,0 @@ +-hisat2/align: +- - modules/nf-core/hisat2/align/** +- - modules/nf-core/hisat2/build/** +- - modules/nf-core/hisat2/extractsplicesites/** + +Changes in 'hisat2/align/tests/main.nf.test': --- modules/nf-core/hisat2/align/tests/main.nf.test +++ modules/nf-core/hisat2/align/tests/main.nf.test @@ -3,12 +3,6 @@ @@ -46,12 +60,4 @@ Changes in module 'nf-core/hisat2/align' test("Single-End") { ---- modules/nf-core/hisat2/align/tests/tags.yml -+++ /dev/null -@@ -1,4 +0,0 @@ --hisat2/align: -- - modules/nf-core/hisat2/align/** -- - modules/nf-core/hisat2/build/** -- - modules/nf-core/hisat2/extractsplicesites/** - ************************************************************ diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml index b23eab75b..d869c5d56 100644 --- a/modules/nf-core/hisat2/align/meta.yml +++ b/modules/nf-core/hisat2/align/meta.yml @@ -7,58 +7,79 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - index: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - summary: - type: file - description: Aligment log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Aligment log + pattern: "*.log" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Output FastQ file + pattern: "*fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml index 6c28eb21c..3272f8e05 100644 --- a/modules/nf-core/hisat2/build/meta.yml +++ b/modules/nf-core/hisat2/build/meta.yml @@ -8,53 +8,58 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fa,fasta,fna}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fa,fasta,fna}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - hisat2: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml index 40d77ce00..c1bdc9e65 100644 --- a/modules/nf-core/hisat2/extractsplicesites/meta.yml +++ b/modules/nf-core/hisat2/extractsplicesites/meta.yml @@ -7,35 +7,40 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] + - txt: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - "*.splice_sites.txt": + type: file + description: Splice sites in txt file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{splice_sites.txt}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 27be64918..773f42484 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto=0.51.1 diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index bbd226c93..73a5f7a95 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -4,8 +4,8 @@ process KALLISTO_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.48.0--h15996b6_2': - 'biocontainers/kallisto:0.48.0--h15996b6_2' }" + 'https://depot.galaxyproject.org/singularity/kallisto:0.51.1--heb0cbe2_0': + 'biocontainers/kallisto:0.51.1--heb0cbe2_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml index d366aeb45..4541074ed 100644 --- a/modules/nf-core/kallisto/index/meta.yml +++ b/modules/nf-core/kallisto/index/meta.yml @@ -6,35 +6,40 @@ keywords: - index tools: - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. + description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq + data, or more generally of target sequences using high-throughput sequencing + reads. homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto licence: ["BSD-2-Clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: genome fasta file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: genome fasta file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - index: - type: directory - description: Kallisto genome index - pattern: "*.idx" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - kallisto: + type: directory + description: Kallisto genome index + pattern: "*.idx" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test b/modules/nf-core/kallisto/index/tests/main.nf.test index c5e86e87c..bdb824012 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test +++ b/modules/nf-core/kallisto/index/tests/main.nf.test @@ -20,7 +20,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.index.get(0).get(1)).exists() }, + { assert snapshot(process.out.versions).match() } ) } } diff --git a/modules/nf-core/kallisto/index/tests/main.nf.test.snap b/modules/nf-core/kallisto/index/tests/main.nf.test.snap index b2891a4a3..42ba6c310 100644 --- a/modules/nf-core/kallisto/index/tests/main.nf.test.snap +++ b/modules/nf-core/kallisto/index/tests/main.nf.test.snap @@ -13,7 +13,7 @@ ] ], "1": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" + "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" ], "index": [ [ @@ -26,47 +26,26 @@ ] ], "versions": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" + "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:27:54.464205" + "timestamp": "2024-10-19T18:51:55.402665844" }, "sarscov2 transcriptome.fasta": { "content": [ - { - "0": [ - [ - { - "id": "transcriptome" - }, - "kallisto:md5,ba657b396f8449f5c85b0563cdaa8346" - ] - ], - "1": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" - ], - "index": [ - [ - { - "id": "transcriptome" - }, - "kallisto:md5,ba657b396f8449f5c85b0563cdaa8346" - ] - ], - "versions": [ - "versions.yml:md5,178f9b57d4228edc356911d571b958a4" - ] - } + [ + "versions.yml:md5,e23afe0f9a5d0dc20b05c27fe59ad041" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-19T09:17:56.733532" + "timestamp": "2024-10-19T18:51:42.328144373" } } \ No newline at end of file diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index 27be64918..773f42484 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::kallisto=0.48.0 + - bioconda::kallisto=0.51.1 diff --git a/modules/nf-core/kallisto/quant/main.nf b/modules/nf-core/kallisto/quant/main.nf index acfc8c9c7..edd0fb203 100644 --- a/modules/nf-core/kallisto/quant/main.nf +++ b/modules/nf-core/kallisto/quant/main.nf @@ -4,8 +4,8 @@ process KALLISTO_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.48.0--h15996b6_2': - 'biocontainers/kallisto:0.48.0--h15996b6_2' }" + 'https://depot.galaxyproject.org/singularity/kallisto:0.51.1--heb0cbe2_0': + 'biocontainers/kallisto:0.51.1--heb0cbe2_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/kallisto/quant/meta.yml b/modules/nf-core/kallisto/quant/meta.yml index d5100290f..329268a17 100644 --- a/modules/nf-core/kallisto/quant/meta.yml +++ b/modules/nf-core/kallisto/quant/meta.yml @@ -6,71 +6,85 @@ keywords: - pseudoalignment tools: - "kallisto": - description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads." + description: "Quantifying abundances of transcripts from RNA-Seq data, or more + generally of target sequences using high-throughput sequencing reads." homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto doi: "10.1038/nbt.3519" licence: ["BSD_2_clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fastq,fastq.gz}" - - index: - type: file - description: Kallisto genome index. - pattern: "*.idx" - - gtf: - type: file - description: Optional gtf file for translation of transcripts into genomic coordinates. - pattern: "*.gtf" - - chromosomes: - type: file - description: Optional tab separated file with chromosome names and lengths. - pattern: "*.tsv" - - fragment_length: - type: integer - description: For single-end mode only, the estimated average fragment length. - - fragment_length_sd: - type: integer - description: For single-end mode only, the estimated standard deviation of the fragment length. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fastq,fastq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Kallisto genome index. + pattern: "*.idx" + - - gtf: + type: file + description: Optional gtf file for translation of transcripts into genomic coordinates. + pattern: "*.gtf" + - - chromosomes: + type: file + description: Optional tab separated file with chromosome names and lengths. + pattern: "*.tsv" + - - fragment_length: + type: integer + description: For single-end mode only, the estimated average fragment length. + - - fragment_length_sd: + type: integer + description: For single-end mode only, the estimated standard deviation of the + fragment length. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Kallisto output file + - json_info: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.run_info.json": + type: file + description: JSON file containing information about the run + pattern: "*.run_info.json" - log: - type: file - description: File containing log information from running kallisto quant - pattern: "*.log.txt" - - abundance: - type: file - description: Plaintext file of the abundance estimates - pattern: "abundance.tsv" - - abundance_hdf5: - type: file - description: | - A HDF5 binary file containing run info, abundance estimates, bootstrap - estimates, and transcript length information - pattern: "abundance.h5" - - run_info: - type: file - description: A json file containing information about the run - pattern: "run_info.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File containing log information from running kallisto quant + pattern: "*.log.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/kallisto/quant/tests/main.nf.test.snap b/modules/nf-core/kallisto/quant/tests/main.nf.test.snap index cf0d73304..db1aa10e6 100644 --- a/modules/nf-core/kallisto/quant/tests/main.nf.test.snap +++ b/modules/nf-core/kallisto/quant/tests/main.nf.test.snap @@ -8,18 +8,18 @@ "id": "test", "single_end": false }, - "test.log:md5,8a5987f8e779cd12ca708e2212f771f5" + "test.log:md5,cb46ef02463f63fec5aac31a4adcac94" ] ], [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:25:27.043048" + "timestamp": "2024-10-19T16:46:09.603634413" }, "sarscov2 paired-end - stub": { "content": [ @@ -54,7 +54,7 @@ ] ], "3": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ], "json_info": [ [ @@ -86,15 +86,15 @@ ] ], "versions": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:26:04.484652" + "timestamp": "2024-10-19T16:46:38.620702213" }, "sarscov2 single-end - stub": { "content": [ @@ -129,7 +129,7 @@ ] ], "3": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ], "json_info": [ [ @@ -161,15 +161,15 @@ ] ], "versions": [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:25:46.479136" + "timestamp": "2024-10-19T16:46:24.255840154" }, "sarscov2 single-end": { "content": [ @@ -180,17 +180,17 @@ "id": "test", "single_end": true }, - "test.log:md5,9c166f0c50cd4fdbdbf1bff9d5d8aba2" + "test.log:md5,0cad96e4108b2ea1c152ad063198b21f" ] ], [ - "versions.yml:md5,f981ad0cc089194a8fb00a47948eea94" + "versions.yml:md5,9956d7fa99ceece8d7ea0ec3e780d970" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:25:08.348876" + "timestamp": "2024-10-19T16:45:56.782215718" } } \ No newline at end of file diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml index 0c067feeb..ba776d315 100644 --- a/modules/nf-core/kraken2/kraken2/environment.yml +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -1,8 +1,6 @@ -name: kraken2_kraken2 channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml index 7909ffe7e..869376467 100644 --- a/modules/nf-core/kraken2/kraken2/meta.yml +++ b/modules/nf-core/kraken2/kraken2/meta.yml @@ -13,63 +13,84 @@ tools: documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - db: - type: directory - description: Kraken2 database - - save_output_fastqs: - type: string - description: | - If true, optional commands are added to save classified and unclassified reads - as fastq files - - save_reads_assignment: - type: string - description: | - If true, an optional command is added to save a file reporting the taxonomic - classification of each input read + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - db: + type: directory + description: Kraken2 database + - - save_output_fastqs: + type: string + description: | + If true, optional commands are added to save classified and unclassified reads + as fastq files + - - save_reads_assignment: + type: string + description: | + If true, an optional command is added to save a file reporting the taxonomic + classification of each input read output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classified_reads_fastq: - type: file - description: | - Reads classified as belonging to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.classified{.,_}*": + type: file + description: | + Reads classified as belonging to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - unclassified_reads_fastq: - type: file - description: | - Reads not classified to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unclassified{.,_}*": + type: file + description: | + Reads not classified to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - classified_reads_assignment: - type: file - description: | - Kraken2 output file indicating the taxonomic assignment of - each input read + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classifiedreads.txt": + type: file + description: | + Kraken2 output file indicating the taxonomic assignment of + each input read - report: - type: file - description: | - Kraken2 report containing stats about classified - and not classifed reads. - pattern: "*.{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: | + Kraken2 report containing stats about classified + and not classifed reads. + pattern: "*.{report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index c0843df29..60adc5ef0 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -2,11 +2,6 @@ nextflow_process { name "Test Process KRAKEN2_KRAKEN2" script "../main.nf" process "KRAKEN2_KRAKEN2" - tag "modules" - tag "modules_nfcore" - tag "untar" - tag "kraken2" - tag "kraken2/kraken2" setup { run("UNTAR") { diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 926d7aece..6300d3f33 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::preseq=3.1.2 + - bioconda::preseq=3.2.0 diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 3fec468e9..540a5fb27 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -5,8 +5,8 @@ process PRESEQ_LCEXTRAP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - 'biocontainers/preseq:3.1.2--h445547b_2' }" + 'https://depot.galaxyproject.org/singularity/preseq:3.2.0--hdcf5f25_6': + 'biocontainers/preseq:3.2.0--hdcf5f25_6' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/preseq/lcextrap/meta.yml b/modules/nf-core/preseq/lcextrap/meta.yml index c00fa8eef..28fb449ca 100644 --- a/modules/nf-core/preseq/lcextrap/meta.yml +++ b/modules/nf-core/preseq/lcextrap/meta.yml @@ -1,44 +1,55 @@ name: preseq_lcextrap -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq licence: ["GPL"] + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lc_extrap: - type: file - description: File containing output of Preseq lcextrap - pattern: "*.{lc_extrap.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lc_extrap.txt": + type: file + description: File containing output of Preseq lcextrap + pattern: "*.{lc_extrap.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap index 3f95cd498..c725d8e89 100644 --- a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap @@ -30,14 +30,14 @@ "single_end - versions": { "content": [ [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T17:20:40.74601" + "timestamp": "2024-10-19T16:55:55.821665692" }, "sarscov2 - single_end - stub": { "content": [ @@ -61,7 +61,7 @@ ] ], "2": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ], "lc_extrap": [ [ @@ -82,27 +82,27 @@ ] ], "versions": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T18:43:12.689062" + "timestamp": "2024-10-19T16:56:11.779385911" }, "paired_end - versions": { "content": [ [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T17:20:52.02843" + "timestamp": "2024-10-19T16:56:31.353046182" }, "single_end - log": { "content": [ @@ -154,7 +154,7 @@ ] ], "2": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ], "lc_extrap": [ [ @@ -175,14 +175,14 @@ ] ], "versions": [ - "versions.yml:md5,9a62ff1c212c53573808ccd2137b8922" + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T18:43:32.569811" + "timestamp": "2024-10-19T16:56:45.034808313" } } \ No newline at end of file diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml index 6f766e4f5..a730261b5 100644 --- a/modules/nf-core/qualimap/rnaseq/meta.yml +++ b/modules/nf-core/qualimap/rnaseq/meta.yml @@ -15,39 +15,42 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/rsem/calculateexpression/meta.yml b/modules/nf-core/rsem/calculateexpression/meta.yml index e6d580e9b..0a7fbe1b3 100644 --- a/modules/nf-core/rsem/calculateexpression/meta.yml +++ b/modules/nf-core/rsem/calculateexpression/meta.yml @@ -12,53 +12,97 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input reads for quantification - pattern: "*.fastq.gz" - - index: - type: file - description: RSEM index - pattern: "rsem/*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input reads for quantification + pattern: "*.fastq.gz" + - - index: + type: file + description: RSEM index + pattern: "rsem/*" output: - counts_gene: - type: file - description: Expression counts on gene level - pattern: "*.genes.results" - - counts_transctips: - type: file - description: Expression counts on transcript level - pattern: "*.isoforms.results" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.genes.results": + type: file + description: Expression counts on gene level + pattern: "*.genes.results" + - counts_transcript: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.isoforms.results": + type: file + description: Expression counts on transcript level + pattern: "*.isoforms.results" - stat: - type: file - description: RSEM statistics - pattern: "*.stat" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.stat": + type: file + description: RSEM statistics + pattern: "*.stat" - logs: - type: file - description: RSEM logs - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: RSEM logs + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - bam_star: - type: file - description: BAM file generated by STAR (optional) - pattern: "*.STAR.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.STAR.genome.bam": + type: file + description: BAM file generated by STAR (optional) + pattern: "*.STAR.genome.bam" - bam_genome: - type: file - description: Genome BAM file (optional) - pattern: "*.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.genome.bam: + type: file + description: Genome BAM file (optional) + pattern: "*.genome.bam" - bam_transcript: - type: file - description: Transcript BAM file (optional) - pattern: "*.transcript.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.transcript.bam: + type: file + description: Transcript BAM file (optional) + pattern: "*.transcript.bam" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rsem/preparereference/meta.yml b/modules/nf-core/rsem/preparereference/meta.yml index 05aa44fe6..e95f4a2ae 100644 --- a/modules/nf-core/rsem/preparereference/meta.yml +++ b/modules/nf-core/rsem/preparereference/meta.yml @@ -12,28 +12,32 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - fasta: - type: file - description: The Fasta file of the reference genome - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: The GTF file of the reference genome - pattern: "*.gtf" + - - fasta: + type: file + description: The Fasta file of the reference genome + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: The GTF file of the reference genome + pattern: "*.gtf" output: - - rsem: - type: directory - description: RSEM index directory - pattern: "rsem" + - index: + - rsem: + type: directory + description: RSEM index directory + pattern: "rsem" - transcript_fasta: - type: file - description: Fasta file of transcripts - pattern: "rsem/*transcripts.fa" + - "*transcripts.fa": + type: file + description: Fasta file of transcripts + pattern: "rsem/*transcripts.fa" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/bamstat/meta.yml b/modules/nf-core/rseqc/bamstat/meta.yml index 72745310c..d69f05442 100644 --- a/modules/nf-core/rseqc/bamstat/meta.yml +++ b/modules/nf-core/rseqc/bamstat/meta.yml @@ -13,25 +13,32 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" output: - txt: - type: file - description: bam statistics report - pattern: "*.bam_stat.txt" + - meta: + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" + - "*.bam_stat.txt": + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/bamstat/tests/main.nf.test b/modules/nf-core/rseqc/bamstat/tests/main.nf.test index fd6fc0811..7af50092d 100644 --- a/modules/nf-core/rseqc/bamstat/tests/main.nf.test +++ b/modules/nf-core/rseqc/bamstat/tests/main.nf.test @@ -3,6 +3,8 @@ nextflow_process { name "Test Process RSEQC_BAMSTAT" script "../main.nf" process "RSEQC_BAMSTAT" + + config "./nextflow.config" test("sarscov2 - [meta] - bam") { diff --git a/modules/nf-core/rseqc/inferexperiment/meta.yml b/modules/nf-core/rseqc/inferexperiment/meta.yml index d9b9ff63e..3ac757289 100644 --- a/modules/nf-core/rseqc/inferexperiment/meta.yml +++ b/modules/nf-core/rseqc/inferexperiment/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: infer_experiment results report - pattern: "*.infer_experiment.txt" + - meta: + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" + - "*.infer_experiment.txt": + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test index 375f65357..37eb8b1f5 100644 --- a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test +++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test @@ -5,6 +5,7 @@ nextflow_process { process "RSEQC_INFEREXPERIMENT" config "./nextflow.config" + test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/innerdistance/meta.yml b/modules/nf-core/rseqc/innerdistance/meta.yml index d0a5bf181..358e4d160 100644 --- a/modules/nf-core/rseqc/innerdistance/meta.yml +++ b/modules/nf-core/rseqc/innerdistance/meta.yml @@ -13,45 +13,72 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - distance: - type: file - description: the inner distances - pattern: "*.inner_distance.txt" + - meta: + type: file + description: the inner distances + pattern: "*.inner_distance.txt" + - "*distance.txt": + type: file + description: the inner distances + pattern: "*.inner_distance.txt" - freq: - type: file - description: frequencies of different insert sizes - pattern: "*.inner_distance_freq.txt" + - meta: + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" + - "*freq.txt": + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" - mean: - type: file - description: mean/median values of inner distances - pattern: "*.inner_distance_mean.txt" + - meta: + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" + - "*mean.txt": + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" - pdf: - type: file - description: distribution plot of inner distances - pattern: "*.inner_distance_plot.pdf" + - meta: + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" + - "*.pdf": + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.inner_distance_plot.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test index e54036f8a..633d27d12 100644 --- a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test +++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test @@ -5,6 +5,7 @@ nextflow_process { process "RSEQC_INNERDISTANCE" config "./nextflow.config" + test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/junctionannotation/meta.yml b/modules/nf-core/rseqc/junctionannotation/meta.yml index a88aa2db3..0622ee43b 100644 --- a/modules/nf-core/rseqc/junctionannotation/meta.yml +++ b/modules/nf-core/rseqc/junctionannotation/meta.yml @@ -13,53 +13,90 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: + - xls: + - meta: + type: file + description: xls file with junction information + pattern: "*.xls" + - "*.xls": + type: file + description: xls file with junction information + pattern: "*.xls" + - rscript: + - meta: + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - "*.r": + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - log: + - meta: + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" + - "*.log": + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" - bed: - type: file - description: bed file of annotated junctions - pattern: "*.junction.bed" + - meta: + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" + - "*.junction.bed": + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" - interact_bed: - type: file - description: Interact bed file - pattern: "*.Interact.bed" - - xls: - type: file - description: xls file with junction information - pattern: "*.xls" + - meta: + type: file + description: Interact bed file + pattern: "*.Interact.bed" + - "*.Interact.bed": + type: file + description: Interact bed file + pattern: "*.Interact.bed" - pdf: - type: file - description: junction plot - pattern: "*.junction.pdf" + - meta: + type: file + description: junction plot + pattern: "*.junction.pdf" + - "*junction.pdf": + type: file + description: junction plot + pattern: "*.junction.pdf" - events_pdf: - type: file - description: events plot - pattern: "*.events.pdf" - - rscript: - type: file - description: Rscript to reproduce the plots - pattern: "*.r" - - log: - type: file - description: Log file of execution - pattern: "*.junction_annotation.log" + - meta: + type: file + description: events plot + pattern: "*.events.pdf" + - "*events.pdf": + type: file + description: events plot + pattern: "*.events.pdf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test index 8a05bccab..b0e4eb86c 100644 --- a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONANNOTATION" + test("sarscov2 - paired end [bam]") { when { diff --git a/modules/nf-core/rseqc/junctionsaturation/meta.yml b/modules/nf-core/rseqc/junctionsaturation/meta.yml index 19ae3f52d..b6f422dc7 100644 --- a/modules/nf-core/rseqc/junctionsaturation/meta.yml +++ b/modules/nf-core/rseqc/junctionsaturation/meta.yml @@ -13,33 +13,45 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - pdf: - type: file - description: Junction saturation report - pattern: "*.pdf" + - meta: + type: file + description: Junction saturation report + pattern: "*.pdf" + - "*.pdf": + type: file + description: Junction saturation report + pattern: "*.pdf" - rscript: - type: file - description: Junction saturation R-script - pattern: "*.r" + - meta: + type: file + description: Junction saturation R-script + pattern: "*.r" + - "*.r": + type: file + description: Junction saturation R-script + pattern: "*.r" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test index 69d7f0c5d..311125576 100644 --- a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONSATURATION" + test("sarscov2 paired-end [bam]") { when { diff --git a/modules/nf-core/rseqc/readdistribution/meta.yml b/modules/nf-core/rseqc/readdistribution/meta.yml index 989792faa..578200abb 100644 --- a/modules/nf-core/rseqc/readdistribution/meta.yml +++ b/modules/nf-core/rseqc/readdistribution/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: the read distribution report - pattern: "*.read_distribution.txt" + - meta: + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" + - "*.read_distribution.txt": + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readduplication/meta.yml b/modules/nf-core/rseqc/readduplication/meta.yml index 4b24d3032..ef94122e9 100644 --- a/modules/nf-core/rseqc/readduplication/meta.yml +++ b/modules/nf-core/rseqc/readduplication/meta.yml @@ -14,41 +14,59 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" output: - seq_xls: - type: file - description: Read duplication rate determined from mapping position of read - pattern: "*seq.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" + - "*seq.DupRate.xls": + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" - pos_xls: - type: file - description: Read duplication rate determined from sequence of read - pattern: "*pos.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" + - "*pos.DupRate.xls": + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" - pdf: - type: file - description: plot of duplication rate - pattern: "*.pdf" + - meta: + type: file + description: plot of duplication rate + pattern: "*.pdf" + - "*.pdf": + type: file + description: plot of duplication rate + pattern: "*.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/tin/meta.yml b/modules/nf-core/rseqc/tin/meta.yml index f760bb2f4..6e363ecd8 100644 --- a/modules/nf-core/rseqc/tin/meta.yml +++ b/modules/nf-core/rseqc/tin/meta.yml @@ -13,37 +13,49 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - bai: - type: file - description: Index for input BAM file - pattern: "*.{bai}" - - bed: - type: file - description: BED file containing the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Index for input BAM file + pattern: "*.{bai}" + - - bed: + type: file + description: BED file containing the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: TXT file containing tin.py results summary - pattern: "*.txt" + - meta: + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" + - "*.txt": + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" - xls: - type: file - description: XLS file containing tin.py results - pattern: "*.xls" + - meta: + type: file + description: XLS file containing tin.py results + pattern: "*.xls" + - "*.xls": + type: file + description: XLS file containing tin.py results + pattern: "*.xls" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index 471164faa..b3f75777e 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index e755d9a34..3d653c0d0 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -4,8 +4,8 @@ process SALMON_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: path genome_fasta diff --git a/modules/nf-core/salmon/index/meta.yml b/modules/nf-core/salmon/index/meta.yml index fd94dd274..48486a2bb 100644 --- a/modules/nf-core/salmon/index/meta.yml +++ b/modules/nf-core/salmon/index/meta.yml @@ -13,22 +13,25 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - genome_fasta: - type: file - description: Fasta file of the reference genome - - transcriptome_fasta: - type: file - description: Fasta file of the reference transcriptome + - - genome_fasta: + type: file + description: Fasta file of the reference genome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome output: - index: - type: directory - description: Folder containing the star index files - pattern: "salmon" + - salmon: + type: directory + description: Folder containing the star index files + pattern: "salmon" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap index 703e455c5..e5899b511 100644 --- a/modules/nf-core/salmon/index/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap @@ -2,25 +2,25 @@ "versions": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-22T14:26:33.32036" + "timestamp": "2024-10-18T10:00:47.087293189" }, "versions stub": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-23T09:47:58.828124" + "timestamp": "2024-10-18T10:01:03.89824494" } } \ No newline at end of file diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 471164faa..b3f75777e 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 6c528b240..f1e3b5cda 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -4,8 +4,8 @@ process SALMON_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml index a2faf589a..4cacde0f0 100644 --- a/modules/nf-core/salmon/quant/meta.yml +++ b/modules/nf-core/salmon/quant/meta.yml @@ -13,47 +13,69 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files for single-end or paired-end data. - Multiple single-end fastqs or pairs of paired-end fastqs are - handled. - - index: - type: directory - description: Folder containing the star index files - - gtf: - type: file - description: GTF of the reference transcriptome - - transcript_fasta: - type: file - description: Fasta file of the reference transcriptome - - alignment_mode: - type: boolean - description: whether to run salmon in alignment mode - - lib_type: - type: string - description: | - Override library type inferred based on strandedness defined in meta object + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files for single-end or paired-end data. + Multiple single-end fastqs or pairs of paired-end fastqs are + handled. + - - index: + type: directory + description: Folder containing the star index files + - - gtf: + type: file + description: GTF of the reference transcriptome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome + - - alignment_mode: + type: boolean + description: whether to run salmon in alignment mode + - - lib_type: + type: string + description: | + Override library type inferred based on strandedness defined in meta object output: - results: - type: directory - description: Folder containing the quantification results for a specific sample - pattern: "${prefix}" + - meta: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" + - ${prefix}: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" - json_info: - type: file - description: File containing meta information from Salmon quant - pattern: "*info.json" + - meta: + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - "*info.json": + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - lib_format_counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*lib_format_counts.json": + type: file + description: File containing the library format counts + pattern: "*lib_format_counts.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap index 547ce2de1..ea22a80ce 100644 --- a/modules/nf-core/salmon/quant/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - single_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -15,15 +15,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:22.424672" + "timestamp": "2024-10-18T10:01:16.989080539" }, "sarscov2 - single_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -36,15 +36,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:32.292277" + "timestamp": "2024-10-18T10:01:29.340996235" }, "sarscov2 - single_end lib type A": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -57,15 +57,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:42.656382" + "timestamp": "2024-10-18T10:01:43.056167576" }, "sarscov2 - pair_end multiple": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -78,15 +78,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:33.03647" + "timestamp": "2024-10-18T10:03:05.500792631" }, "sarscov2 - pair_end multiple stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -99,15 +99,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:43.388379" + "timestamp": "2024-10-18T10:03:26.428959203" }, "sarscov2 - single_end lib type A stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -120,15 +120,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:52.612664" + "timestamp": "2024-10-18T10:02:03.420850208" }, "sarscov2 - pair_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -141,15 +141,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:05.577881" + "timestamp": "2024-10-18T10:02:16.130074696" }, "sarscov2 - pair_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -162,9 +162,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:15.286461" + "timestamp": "2024-10-18T10:02:39.470004547" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 754d84b73..4a4997274 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 97991358e..cdc4c2544 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,5 +1,6 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG + type keywords: - stats - mapping @@ -17,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flagstat": + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 23989c612..04c3852b2 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:28.002887" + "timestamp": "2024-09-16T08:02:58.866491759" }, "BAM": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:13.330971" + "timestamp": "2024-09-16T08:02:47.383332837" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 2ea2a5ccd..c4b5a0a3f 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 344e92a3f..f0a6bcb2a 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -18,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idxstats": + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a5ac8104e..2cc89a3b8 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:56.180093" + "timestamp": "2024-09-16T08:11:56.466856235" }, "bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:41.408704" + "timestamp": "2024-09-16T08:11:46.311550359" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b9..311756102 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03e..db8df0d50 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,38 +15,52 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199ce..72d65e81a 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:53.9057" + "timestamp": "2024-09-16T08:21:25.261127166" }, "crai - stub": { "content": [ @@ -65,7 +65,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:45.931558" + "timestamp": "2024-09-16T08:21:12.653194876" }, "bai - stub": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -130,28 +130,28 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:34.807525" + "timestamp": "2024-09-16T08:21:01.854932651" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:52:55.688799" + "timestamp": "2024-09-16T08:20:51.485364222" }, "crai": { "content": [ @@ -172,7 +172,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -190,15 +190,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:17.609533" + "timestamp": "2024-09-16T08:20:40.518873972" }, "bai": { "content": [ @@ -219,7 +219,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -237,14 +237,14 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:04.16585" + "timestamp": "2024-09-16T08:20:21.184050361" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099c..caf3c61a8 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,19 +4,19 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta) , path(bam) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0eb..a9dbec5a8 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,52 +15,73 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file(s) - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta,fna}" - optional: true + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 41c2fca7f..14d9d73d8 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -35,6 +35,40 @@ nextflow_process { } } + test("multiple bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + test("cram") { config "./nextflow_cram.config" @@ -94,6 +128,36 @@ nextflow_process { } } + test("multiple bam - stub") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("cram - stub") { options "-stub" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index da38d5d15..469891fe3 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:19:37.196205" + "timestamp": "2024-09-16T08:49:58.207549273" }, "bam - stub": { "content": [ @@ -57,7 +57,7 @@ ] ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -84,15 +84,15 @@ ] ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:46.580756" + "timestamp": "2024-09-16T08:50:08.630951018" }, "cram - stub": { "content": [ @@ -122,7 +122,7 @@ ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ @@ -149,15 +149,110 @@ ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-09-16T08:50:19.061912443" + }, + "multiple bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:59:55.479443" + }, + "multiple bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:36:13.781404" }, "bam": { "content": [ @@ -167,7 +262,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" ] ], [ @@ -180,13 +275,13 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.09.0" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-10-08T11:59:46.372244" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index da2df5e43..62054fc97 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 982bc28e7..493525a9e 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 735ff8122..77b020f76 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -16,43 +16,46 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing samtools stats output + pattern: "*.{stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index 6416ae127..ea8a233de 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "SAMTOOLS_STATS" + test("bam") { when { diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 3828f3788..df507be7a 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:24.885816" + "timestamp": "2024-09-16T09:29:16.767396182" }, "bam - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:39.310713" + "timestamp": "2024-09-16T09:29:29.721580274" }, "cram - stub": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:21:04.771199" + "timestamp": "2024-09-16T09:29:53.567964304" }, "bam": { "content": [ @@ -113,11 +113,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -125,18 +125,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:19:06.645466" + "timestamp": "2024-09-16T09:28:50.73610604" } } \ No newline at end of file diff --git a/modules/nf-core/sortmerna/meta.yml b/modules/nf-core/sortmerna/meta.yml index c0a2a581f..3b43d006d 100644 --- a/modules/nf-core/sortmerna/meta.yml +++ b/modules/nf-core/sortmerna/meta.yml @@ -8,67 +8,84 @@ keywords: - ribosomal RNA tools: - SortMeRNA: - description: The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. + description: The core algorithm is based on approximate seeds and allows for sensitive + analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from + metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, + fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart + aligned and rejected reads into two files. Additional applications include clustering + and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with + Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. homepage: https://hpc.nih.gov/apps/sortmeRNA.html documentation: https://github.com/biocore/sortmerna/wiki/ licence: ["GPL-3.0-or-later"] + identifier: biotools:sortmerna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fastas: - type: file - description: | - Path to reference file(s) - - meta3: - type: map - description: | - Groovy Map containing index information - e.g. [ id:'test' ] - - index: - type: directory - description: | - Path to index directory of a previous sortmerna run + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fastas: + type: file + description: | + Path to reference file(s) + - - meta3: + type: map + description: | + Groovy Map containing index information + e.g. [ id:'test' ] + - index: + type: directory + description: | + Path to index directory of a previous sortmerna run output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ], or reference information from an - indexing-only run - reads: - type: file - description: The filtered fastq reads - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*non_rRNA.fastq.gz": + type: file + description: The filtered fastq reads + pattern: "*fastq.gz" - log: - type: file - description: SortMeRNA log file - pattern: "*sortmerna.log" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*.log": + type: file + description: SortMeRNA log file + pattern: "*sortmerna.log" - index: - type: directory - description: | - Path to index directory generated by sortmern + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - idx: + type: directory + description: | + Path to index directory generated by sortmern - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@mashehu" diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test index 1954bdfb0..4388cda0c 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test +++ b/modules/nf-core/sortmerna/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_process { process "SORTMERNA" test("sarscov2 indexing only") { - + config './indexing_only.config' when { diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index e3d1c714d..1debc4c9b 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - bioconda::htslib=1.18 + - bioconda::samtools=1.18 + - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index ae67e0040..b5bc9ddf8 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -21,33 +21,34 @@ process STAR_ALIGN { tuple val(meta), path('*Log.progress.out'), emit: log_progress path "versions.yml" , emit: versions - tuple val(meta), path('*d.out.bam') , optional:true, emit: bam - tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted - tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript - tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted - tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq - tuple val(meta), path('*.tab') , optional:true, emit: tab - tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab - tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab - tuple val(meta), path('*.out.junction') , optional:true, emit: junction - tuple val(meta), path('*.out.sam') , optional:true, emit: sam - tuple val(meta), path('*.wig') , optional:true, emit: wig - tuple val(meta), path('*.bg') , optional:true, emit: bedgraph + tuple val(meta), path('*d.out.bam') , optional:true, emit: bam + tuple val(meta), path("${prefix}.sortedByCoord.out.bam") , optional:true, emit: bam_sorted + tuple val(meta), path("${prefix}.Aligned.sortedByCoord.out.bam") , optional:true, emit: bam_sorted_aligned + tuple val(meta), path('*toTranscriptome.out.bam') , optional:true, emit: bam_transcript + tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted + tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq + tuple val(meta), path('*.tab') , optional:true, emit: tab + tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab + tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab + tuple val(meta), path('*.out.junction') , optional:true, emit: junction + tuple val(meta), path('*.out.sam') , optional:true, emit: sam + tuple val(meta), path('*.wig') , optional:true, emit: wig + tuple val(meta), path('*.bg') , optional:true, emit: bedgraph when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def reads1 = [], reads2 = [] meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" def seq_center = seq_center ? "'CN:$seq_center'" : "" - def attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" + attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' - def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' + mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ STAR \\ --genomeDir $index \\ @@ -79,7 +80,7 @@ process STAR_ALIGN { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ echo "" | gzip > ${prefix}.unmapped_1.fastq.gz echo "" | gzip > ${prefix}.unmapped_2.fastq.gz diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index e80dbb7dd..5cfe763e3 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -14,97 +14,212 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: - type: directory - description: STAR genome index - pattern: "star" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - star_ignore_sjdbgtf: - type: boolean - description: Ignore annotation GTF file - - seq_platform: - type: string - description: Sequencing platform - - seq_center: - type: string - description: Sequencing center + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - index: + type: directory + description: STAR genome index + pattern: "star" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - - seq_platform: + type: string + description: Sequencing platform + - - seq_center: + type: string + description: Sequencing center output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*d.out.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bam_sorted: - type: file - description: Sorted BAM file of read alignments (optional) - pattern: "*sortedByCoord.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sortedByCoord.out.bam: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" + - bam_sorted_aligned: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.Aligned.sortedByCoord.out.bam: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*.Aligned.sortedByCoord.out.bam" - bam_transcript: - type: file - description: Output BAM file of transcriptome alignment (optional) - pattern: "*toTranscriptome.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*toTranscriptome.out.bam": + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" - bam_unsorted: - type: file - description: Unsorted BAM file of read alignments (optional) - pattern: "*Aligned.unsort.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Aligned.unsort.out.bam": + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" - fastq: - type: file - description: Unmapped FastQ files (optional) - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" - tab: - type: file - description: STAR output tab file(s) (optional) - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - spl_junc_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.SJ.out.tab": + type: file + description: STAR output splice junction tab file + pattern: "*.SJ.out.tab" + - read_per_gene_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ReadsPerGene.out.tab": + type: file + description: STAR output read per gene tab file + pattern: "*.ReadsPerGene.out.tab" - junction: - type: file - description: STAR chimeric junction output file (optional) - pattern: "*.out.junction" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out.junction": + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.out.sam" + - "*.out.sam": + type: file + description: STAR output SAM file(s) (optional) + pattern: "*.out.sam" - wig: - type: file - description: STAR output wiggle format file(s) (optional) - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" - bedgraph: - type: file - description: STAR output bedGraph format file(s) (optional) - pattern: "*.bg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bg": + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index c814eb56c..0da28d37c 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -26,7 +26,11 @@ "id": "test", "single_end": true }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -35,7 +39,7 @@ "id": "test", "single_end": true }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -44,7 +48,7 @@ "id": "test", "single_end": true }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -53,7 +57,7 @@ "id": "test", "single_end": true }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -62,10 +66,19 @@ "id": "test", "single_end": true }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -105,10 +118,7 @@ "id": "test", "single_end": true }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -117,7 +127,7 @@ "id": "test", "single_end": true }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -126,7 +136,7 @@ "id": "test", "single_end": true }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -135,10 +145,7 @@ "id": "test", "single_end": true }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -148,9 +155,8 @@ "single_end": true }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -173,10 +179,16 @@ "id": "test", "single_end": true }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -312,7 +324,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:04.712114" + "timestamp": "2024-10-01T11:39:15.440397" }, "homo_sapiens - paired_end - arriba - stub": { "content": [ @@ -341,7 +353,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -350,7 +366,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -359,7 +375,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -368,7 +384,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -377,10 +393,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -420,10 +445,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -432,7 +454,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -441,7 +463,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -450,10 +472,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -463,9 +482,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -488,10 +506,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -627,7 +651,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:28.874293" + "timestamp": "2024-10-01T11:40:15.472109" }, "homo_sapiens - single_end": { "content": [ @@ -644,13 +668,7 @@ ] ], [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535" - ] + ], [ @@ -711,7 +729,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T18:02:34.35338" + "timestamp": "2024-10-01T11:23:08.001162" }, "homo_sapiens - paired_end": { "content": [ @@ -728,13 +746,7 @@ ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] + ], [ @@ -795,7 +807,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T18:03:16.701923" + "timestamp": "2024-10-01T11:24:46.295219" }, "homo_sapiens - paired_end - multiple - stub": { "content": [ @@ -824,7 +836,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -833,7 +849,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -842,7 +858,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -851,7 +867,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -860,10 +876,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -903,10 +928,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -915,7 +937,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -924,7 +946,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -933,10 +955,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -946,9 +965,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -971,10 +989,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1110,7 +1134,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:51.360287" + "timestamp": "2024-10-01T11:41:07.310866" }, "homo_sapiens - paired_end - multiple": { "content": [ @@ -1127,13 +1151,7 @@ ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" - ] + ], [ @@ -1194,7 +1212,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T13:13:28.987438" + "timestamp": "2024-10-01T11:38:46.605044" }, "homo_sapiens - paired_end - stub": { "content": [ @@ -1223,7 +1241,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -1232,7 +1254,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -1241,7 +1263,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -1250,7 +1272,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -1259,10 +1281,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -1302,10 +1333,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -1314,7 +1342,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -1323,7 +1351,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -1332,10 +1360,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -1345,9 +1370,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1370,10 +1394,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1509,7 +1539,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:16.798018" + "timestamp": "2024-10-01T11:39:51.595873" }, "homo_sapiens - paired_end - starfusion": { "content": [ @@ -1584,7 +1614,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T13:10:55.371956" + "timestamp": "2024-10-01T11:35:43.874508" }, "homo_sapiens - paired_end - arriba": { "content": [ @@ -1653,7 +1683,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T13:05:10.7534" + "timestamp": "2024-10-01T11:28:32.599223" }, "homo_sapiens - paired_end - starfusion - stub": { "content": [ @@ -1682,7 +1712,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -1691,7 +1725,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -1700,7 +1734,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -1709,7 +1743,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -1718,10 +1752,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -1761,10 +1804,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -1773,7 +1813,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -1782,7 +1822,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -1791,10 +1831,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -1804,9 +1841,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1829,10 +1865,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1968,6 +2010,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:40.64399" + "timestamp": "2024-10-01T11:40:42.29249" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config index 2324b9e58..cf09323fc 100644 --- a/modules/nf-core/star/align/tests/nextflow.arriba.config +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config index c4ac58088..18bc2ee8a 100644 --- a/modules/nf-core/star/align/tests/nextflow.config +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config index 467b64977..7880bfcf5 100644 --- a/modules/nf-core/star/align/tests/nextflow.starfusion.config +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 38611dfa2..1debc4c9b 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.18 - bioconda::htslib=1.18 + - bioconda::samtools=1.18 - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 1061e1b8d..33c1f65f3 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -14,37 +14,40 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the reference genome - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the reference genome + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: directory - description: Folder containing the star index files - pattern: "star" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - star: + type: directory + description: Folder containing the star index files + pattern: "star" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 0556de41a..906b7486c 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie=2.2.3 diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 6e25ba27d..4635c8c5b 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -4,8 +4,8 @@ process STRINGTIE_STRINGTIE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.3--h43eeafb_0' : + 'biocontainers/stringtie:2.2.3--h43eeafb_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml index d8ebdd88a..e55b2abfc 100644 --- a/modules/nf-core/stringtie/stringtie/meta.yml +++ b/modules/nf-core/stringtie/stringtie/meta.yml @@ -12,46 +12,67 @@ tools: homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual licence: ["MIT"] + identifier: biotools:stringtie input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Stringtie transcript gtf output(s). - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Stringtie transcript gtf output(s). + - - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - transcript_gtf: - type: file - description: transcript gtf - pattern: "*.{transcripts.gtf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.gtf": + type: file + description: transcript gtf + pattern: "*.{transcripts.gtf}" + - abundance: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abundance.txt": + type: file + description: abundance + pattern: "*.{abundance.txt}" - coverage_gtf: - type: file - description: coverage gtf - pattern: "*.{coverage.gtf}" - - abudance: - type: file - description: abudance - pattern: "*.{abudance.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coverage.gtf": + type: file + description: coverage gtf + pattern: "*.{coverage.gtf}" - ballgown: - type: file - description: for running ballgown - pattern: "*.{ballgown}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ballgown": + type: file + description: for running ballgown + pattern: "*.{ballgown}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap index 124dd4cbe..d4645de3e 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -31,18 +31,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + "test.transcripts.gtf:md5,37154e7bda96544f24506ee902bb561d" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:44.299962" + "timestamp": "2024-10-18T09:56:50.294157199" }, "sarscov2 [bam] - forward strandedness": { "content": [ @@ -61,18 +61,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + "test.transcripts.gtf:md5,6087dfc9700a52d9e4a1ae3fcd1d1dfd" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:35.177738" + "timestamp": "2024-10-18T09:56:39.4249133" }, "sarscov2 [bam] - forward strandedness - stub": { "content": [ @@ -114,7 +114,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -153,15 +153,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:32.885078" + "timestamp": "2024-10-18T09:57:23.008470065" }, "sarscov2 [bam] - forward strandedness + reference annotation - stub": { "content": [ @@ -203,7 +203,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -242,15 +242,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:43.325777" + "timestamp": "2024-10-18T09:57:33.622824981" }, "sarscov2 [bam] - reverse strandedness + reference annotation - stub": { "content": [ @@ -292,7 +292,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -331,15 +331,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:37:06.085936" + "timestamp": "2024-10-18T09:57:55.803421433" }, "sarscov2 [bam] - reverse strandedness - stub": { "content": [ @@ -381,7 +381,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -420,15 +420,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:53.837578" + "timestamp": "2024-10-18T09:57:44.825389635" }, "sarscov2 [bam] - reverse strandedness + reference annotation": { "content": [ @@ -462,18 +462,18 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + "test.transcripts.gtf:md5,fbabb4e3888bbede67f11f692e484880" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:34:03.114695" + "timestamp": "2024-10-18T09:57:11.793664242" }, "sarscov2 [bam] - reverse strandedness": { "content": [ @@ -492,17 +492,17 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + "test.transcripts.gtf:md5,01d6da00a3c458420841e57427297183" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:52.874479" + "timestamp": "2024-10-18T09:57:01.166309777" } } \ No newline at end of file diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 7e919aa31..fdb575020 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread=2.0.6 diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 471bd16fd..d51de1e0b 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,8 +4,8 @@ process SUBREAD_FEATURECOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - 'biocontainers/subread:2.0.1--hed695b0_0' }" + 'https://depot.galaxyproject.org/singularity/subread:2.0.6--he4a0461_2' : + 'biocontainers/subread:2.0.6--he4a0461_2' }" input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/subread/featurecounts/meta.yml b/modules/nf-core/subread/featurecounts/meta.yml index 38a379456..a9b045b7d 100644 --- a/modules/nf-core/subread/featurecounts/meta.yml +++ b/modules/nf-core/subread/featurecounts/meta.yml @@ -7,43 +7,55 @@ keywords: - reference tools: - featurecounts: - description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads. + description: featureCounts is a highly efficient general-purpose read summarization + program that counts mapped reads for genomic features such as genes, exons, + promoter, gene bodies, genomic bins and chromosomal locations. It can be used + to count both RNA-seq and genomic DNA-seq reads. homepage: http://bioinf.wehi.edu.au/featureCounts/ documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf doi: "10.1093/bioinformatics/btt656" licence: ["GPL v3"] + identifier: biotools:subread input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - annotation: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf,saf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: BAM files containing mapped reads + pattern: "*.bam" + - annotation: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf,saf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - counts: - type: file - description: Counts of reads mapping to features - pattern: "*featureCounts.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt": + type: file + description: Counts of reads mapping to features + pattern: "*featureCounts.txt" - summary: - type: file - description: Summary log file - pattern: "*.featureCounts.txt.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt.summary": + type: file + description: Summary log file + pattern: "*.featureCounts.txt.summary" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap index 72e8dcddf..5a743f0ce 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap @@ -8,15 +8,15 @@ "single_end": true, "strandedness": "forward" }, - "test.featureCounts.txt:md5,0012df4c0a0e47eec1440017ab34f75f" + "test.featureCounts.txt:md5,4cf89f0e702ba9abef3fa571e68fe8f0" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.685863663" + "timestamp": "2024-10-18T10:19:47.695388295" }, "unstranded_counts": { "content": [ @@ -27,15 +27,15 @@ "single_end": true, "strandedness": "unstranded" }, - "test.featureCounts.txt:md5,3307d31b44a5d6bb3389786bb8f4e91f" + "test.featureCounts.txt:md5,c4ef2c2a80547fbb3074331bc0a1bda3" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.67903701" + "timestamp": "2024-10-18T10:21:03.208334705" }, "reverse_summary": { "content": [ @@ -80,7 +80,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -103,15 +103,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:22.628032" + "timestamp": "2024-10-18T10:20:10.040191252" }, "sarscov2 [bam] - reverse - stub": { "content": [ @@ -137,7 +137,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -160,15 +160,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:52.371212" + "timestamp": "2024-10-18T10:20:42.708101743" }, "reverse_counts": { "content": [ @@ -179,15 +179,15 @@ "single_end": true, "strandedness": "reverse" }, - "test.featureCounts.txt:md5,8175816b8260ed444d59232bd7e7120b" + "test.featureCounts.txt:md5,a7d8843ebc12d855c2e68d3e2e137582" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.160010804" + "timestamp": "2024-10-18T10:20:24.490755916" }, "sarscov2 [bam] - unstranded - stub": { "content": [ @@ -213,7 +213,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -236,15 +236,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:05:25.058902" + "timestamp": "2024-10-18T10:21:19.244837771" }, "forward_summary": { "content": [ @@ -268,14 +268,14 @@ "forward_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.704797013" + "timestamp": "2024-10-18T10:19:48.001158764" }, "unstranded_summary": { "content": [ @@ -299,25 +299,25 @@ "reverse_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.175265594" + "timestamp": "2024-10-18T10:20:24.551053149" }, "unstranded_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.69390501" + "timestamp": "2024-10-18T10:21:03.25895568" } } \ No newline at end of file diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml index e5118d289..820d4f163 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "summarizedexperiment_summarizedexperiment" description: | @@ -11,68 +10,77 @@ keywords: - assay tools: - "summarizedexperiment": - description: "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples." + description: "The SummarizedExperiment container contains one or more assays, + each represented by a matrix-like object of numeric or other mode. The rows + typically represent genomic ranges of interest and the columns represent samples." homepage: "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html" tool_dev_url: "https://github.com/Bioconductor/SummarizedExperiment" doi: "10.18129/B9.bioc.SummarizedExperiment" licence: ["Artistic-2.0"] + identifier: biotools:summarizedexperiment input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - matrix_files: - type: directory - description: | - One or more paths to CSV or TSV matrix files. All files must have the - same rows and columns. - pattern: "*.{csv,tsv}" - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference from which matrix rows are derived e.g. `[ id:'yeast' ]` - - rowdata: - type: file - description: | - Metadata on matrix features. One column must contain all matrix row - IDs. - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole, - as represented by the matrix columns and the sample sheet e.g. - `[id:'SRP123456' ]` - - coldata: - type: file - description: | - Metadata on matrix columns. One column must contain all matrix column - IDs. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - matrix_files: + type: directory + description: | + One or more paths to CSV or TSV matrix files. All files must have the + same rows and columns. + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference from which matrix rows are derived e.g. `[ id:'yeast' ]` + - rowdata: + type: file + description: | + Metadata on matrix features. One column must contain all matrix row + IDs. + pattern: "*.{csv,tsv}" + - - meta3: + type: map + description: | + Groovy Map containing information related to the experiment as a whole, + as represented by the matrix columns and the sample sheet e.g. + `[id:'SRP123456' ]` + - coldata: + type: file + description: | + Metadata on matrix columns. One column must contain all matrix column + IDs. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - rds: - type: file - description: Serialised SummarizedExperiment object - pattern: "*.SummarizedExperiment.rds" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.rds": + type: file + description: Serialised SummarizedExperiment object + pattern: "*.SummarizedExperiment.rds" - log: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test index 8faa18afb..f80f3ee44 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT" + setup { run("UNTAR") { diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index f172c1b39..910ffa882 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=3.4 - - bioconda::trim-galore=0.6.7 + - bioconda::cutadapt=4.2 + - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 0e2f32902..30d17edc1 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 6cb31c9f9..61b3504a9 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:20.401347" + "timestamp": "2024-10-18T12:50:36.440264431" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -77,10 +77,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:27:44.964166" + "timestamp": "2024-10-18T12:50:51.25902234" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -160,21 +160,21 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:28:07.611496" + "timestamp": "2024-10-18T12:51:19.024228479" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:28.960497" + "timestamp": "2024-10-18T12:51:02.471703095" } } \ No newline at end of file diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml index 9ee5fd365..d4c6a5492 100644 --- a/modules/nf-core/tximeta/tximport/meta.yml +++ b/modules/nf-core/tximeta/tximport/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tximeta_tximport" description: | @@ -18,102 +17,131 @@ tools: tool_dev_url: "https://github.com/thelovelab/tximeta" doi: "10.1371/journal.pcbi.1007664" licence: ["GPL-2"] + identifier: biotools:tximeta input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference e.g. `[ id:'yeast' ]` - - tx2gene: - type: file - description: A transcript to gene mapping table such as those generated - by custom/tx2gene - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - coldata: - type: file - description: | - Optional 'coldata' file equivalent to a sample sheet where the first - column corresponds to the sample names (directory names in the input - salmon/ kallisto results) - pattern: "*.{csv,tsv}" - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: directory + description: Directory containing quantification files + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference e.g. `[ id:'yeast' ]` + - tx2gene: + type: file + description: A transcript to gene mapping table such as those generated by custom/tx2gene + pattern: "*.{csv,tsv}" + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - tpm_gene: - type: file - description: | - Abundance (TPM) values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_tpm.tsv" - counts_gene: - type: file - description: | - Count values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts.tsv": + type: file + description: | + Count values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_counts.tsv" - counts_gene_length_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'lengthScaledTPM' - pattern: "*gene_counts_length_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_length_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'lengthScaledTPM' + pattern: "*gene_counts_length_scaled.tsv" - counts_gene_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'scaledTPM' - pattern: "*gene_counts_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'scaledTPM' + pattern: "*gene_counts_scaled.tsv" - lengths_gene: - type: file - description: | - Length values derived from tximport output after summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_lengths.tsv": + type: file + description: | + Length values derived from tximport output after summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - tpm_transcript: - type: file - description: | - Abundance (TPM) values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_tpm.tsv" - counts_transcript: - type: file - description: | - Count values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_counts.tsv": + type: file + description: | + Count values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_counts.tsv" - lengths_transcript: - type: file - description: | - Length values derived from tximport output without summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_lengths.tsv": + type: file + description: | + Length values derived from tximport output without summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test index 782030fb8..d26e54100 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "TXIMETA_TXIMPORT" + test("saccharomyces_cerevisiae - kallisto - gtf") { setup { diff --git a/modules/nf-core/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml index 2467a28f2..9222d31d2 100644 --- a/modules/nf-core/ucsc/bedclip/meta.yml +++ b/modules/nf-core/ucsc/bedclip/meta.yml @@ -9,30 +9,36 @@ tools: description: Remove lines from bed file that refer to off-chromosome locations. homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - - sizes: + type: file + description: Chromosome sizes file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index a54fb8f16..27868a444 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig=469 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index bff0b00a9..81cdee953 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -5,8 +5,8 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:445--h954228d_0' : - 'biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0' }" + 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:469--h9b8f530_0' : + 'biocontainers/ucsc-bedgraphtobigwig:469--h9b8f530_0' }" input: tuple val(meta), path(bedgraph) @@ -22,7 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bedGraphToBigWig \\ $bedgraph \\ @@ -37,7 +37,7 @@ process UCSC_BEDGRAPHTOBIGWIG { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.bigWig diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml index a60118abe..5d42cbde7 100755 --- a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml @@ -12,34 +12,37 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: https://genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedGraph}" - - sizes: - type: file - description: chromosome sizes file - pattern: "*.{sizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedGraph}" + - - sizes: + type: file + description: chromosome sizes file + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigwig: - type: file - description: bigWig file - pattern: "*.{bigWig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigWig": + type: file + description: bigWig file + pattern: "*.{bigWig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap index 7b0181583..7c731f651 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:06:05.176746" + "timestamp": "2024-10-18T10:47:58.558813949" }, "Should run without failures": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:05:56.658148" + "timestamp": "2024-10-18T10:47:36.476844229" } } \ No newline at end of file diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml index 38d3fd465..6cbd84116 100644 --- a/modules/nf-core/umitools/dedup/meta.yml +++ b/modules/nf-core/umitools/dedup/meta.yml @@ -1,5 +1,6 @@ name: umitools_dedup -description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached + to the read. keywords: - umitools - deduplication @@ -7,60 +8,89 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" - - get_output_stats: - type: boolean - description: | - Whether or not to generate output stats. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" + - - get_output_stats: + type: boolean + description: | + Whether or not to generate output stats. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - tsv_edit_distance: - type: file - description: Reports the (binned) average edit distance between the UMIs at each position. - pattern: "*edit_distance.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*edit_distance.tsv": + type: file + description: Reports the (binned) average edit distance between the UMIs at + each position. + pattern: "*edit_distance.tsv" - tsv_per_umi: - type: file - description: UMI-level summary statistics. - pattern: "*per_umi.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_umi.tsv": + type: file + description: UMI-level summary statistics. + pattern: "*per_umi.tsv" - tsv_umi_per_position: - type: file - description: Tabulates the counts for unique combinations of UMI and position. - pattern: "*per_position.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_position.tsv": + type: file + description: Tabulates the counts for unique combinations of UMI and position. + pattern: "*per_position.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test index 883e2d9d7..4ba50c5fe 100644 --- a/modules/nf-core/umitools/dedup/tests/main.nf.test +++ b/modules/nf-core/umitools/dedup/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "UMITOOLS_DEDUP" + test("se - no stats") { config "./nextflow.config" diff --git a/modules/nf-core/umitools/prepareforrsem/meta.yml b/modules/nf-core/umitools/prepareforrsem/meta.yml index 8b85366cc..3e8ead257 100644 --- a/modules/nf-core/umitools/prepareforrsem/meta.yml +++ b/modules/nf-core/umitools/prepareforrsem/meta.yml @@ -8,43 +8,53 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Prepared BAM file. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Prepared BAM file. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@pinin4fjords" diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test index 105093505..4dfb522a3 100644 --- a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test +++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_process { script "../main.nf" process "UMITOOLS_PREPAREFORRSEM" + test("sarscov2 - bam") { when { diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f5..290346b3f 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap index 4fd70b5f3..d39f9129b 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "test" }, - "test.stats:md5,09d1bd8f10e000921202f7ea1cd0679e" + "test.stats:md5,84891a894010aeb882c4092db9248d2c" ] ], [ @@ -26,18 +26,18 @@ ] ], [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T11:53:11.53709" + "timestamp": "2024-09-16T08:04:23.444693448" }, "sarscov2_bam_bai - stub": { "content": [ @@ -67,7 +67,7 @@ ] ], "3": [ - + ], "4": [ [ @@ -94,10 +94,10 @@ ] ], "7": [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ], "bai": [ @@ -117,7 +117,7 @@ ] ], "csi": [ - + ], "deduplog": [ [ @@ -152,18 +152,18 @@ ] ], "versions": [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:34:35.959581" + "timestamp": "2024-09-16T08:04:43.790052381" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test index f023a9f7d..48dbcf2f0 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -4,6 +4,7 @@ nextflow_workflow { script "../main.nf" workflow "BAM_MARKDUPLICATES_PICARD" + test("sarscov2 - bam") { when { diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 32788a18c..50ecf675d 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -2,23 +2,23 @@ "homo_sapiens - cram": { "content": [ "test.cram", - "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e", + "test.cram.crai:md5,9a74bf028b7146d8ef285442a14bbc8f", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", - "test.stats:md5,372a7d9d9081aa009b21343a913beb14", + "test.stats:md5,1a4569080c6f73546a863b0c3bc72c49", [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:28:15.15911" + "timestamp": "2024-10-18T10:59:53.440891602" }, "sarscov2 - bam - stub": { "content": [ @@ -87,11 +87,11 @@ ] ], "9": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ [ @@ -157,19 +157,19 @@ ] ], "versions": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:28:40.128144" + "timestamp": "2024-10-18T11:00:20.860494683" }, "homo_sapiens - cram - stub": { "content": [ @@ -232,11 +232,11 @@ ] ], "9": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -296,39 +296,39 @@ ] ], "versions": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:29:04.075263" + "timestamp": "2024-10-18T11:00:42.042387118" }, "sarscov2 - bam": { "content": [ - "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b", - "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404", + "test.bam:md5,c8a3a56d56bf2c87f09e143ed2f78a7d", + "test.bam.bai:md5,7d205e4e0b3d98887b1eafb5c50a3363", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", - "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574", + "test.stats:md5,ba007b13981dad548358c7c957d41e12", [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,966dcea920866a87b55e665563864fc9", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:27:47.343274" + "timestamp": "2024-10-18T10:59:22.840531827" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index b7f4da177..c3c9a0492 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -25,22 +25,22 @@ "id": "test", "single_end": false }, - "test.stats:md5,d32de3b3716a11039cef2367c3c1a56e" + "test.stats:md5,2fe0f3a7a1f07906061c1dadb62e0d05" ] ], [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:02:44.34964" + "timestamp": "2024-09-16T08:26:24.36986488" }, "test_bam_sort_stats_samtools_paired_end": { "content": [ @@ -68,22 +68,22 @@ "id": "test", "single_end": false }, - "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574" + "test.stats:md5,ba007b13981dad548358c7c957d41e12" ] ], [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:03:02.583095" + "timestamp": "2024-09-16T08:26:38.683996037" }, "test_bam_sort_stats_samtools_single_end - stub": { "content": [ @@ -137,11 +137,11 @@ ] ], "6": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ], "bai": [ [ @@ -192,19 +192,19 @@ ] ], "versions": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:03:22.328703" + "timestamp": "2024-09-16T08:07:18.896460047" }, "test_bam_sort_stats_samtools_paired_end - stub": { "content": [ @@ -258,11 +258,11 @@ ] ], "6": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ], "bai": [ [ @@ -313,18 +313,18 @@ ] ], "versions": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - 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"nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:25.801394" + "timestamp": "2024-09-16T08:07:49.731645858" }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -291,20 +291,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,7afd486ad6abb9a2a3dac90c99e1d87b" + "test.stats:md5,8140d69cdedd77570ca1d7618a744e16" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:36.158768" + "timestamp": "2024-09-16T08:08:01.421996172" }, "test_bam_stats_samtools_paired_end_cram": { "content": [ @@ -332,19 +332,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,16b59a1f2c99d9fe30f711adc3ebe32d" + "test.stats:md5,1622856127bafd6cdbadee9cd64ec9b7" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:46.625907" + "timestamp": "2024-09-16T08:08:12.640915756" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap index 26ed39c00..7bbcf72b7 100644 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ], "bedgraph": [ @@ -43,16 +43,16 @@ ] ], "versions": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-26T01:55:31.016058335" + "timestamp": "2024-10-18T10:48:23.095911334" }, "sarscov2 [bedgraph] [genome_sizes] - stub": { "content": [ @@ -76,7 +76,7 @@ ] ], "2": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ], "bedgraph": [ @@ -98,15 +98,15 @@ ] ], "versions": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:22:51.388076" + "timestamp": "2024-10-18T10:48:45.587883209" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test index 0048b3b33..37dd098cd 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test @@ -5,6 +5,9 @@ nextflow_workflow { workflow "FASTQ_ALIGN_HISAT2" config "./nextflow.config" + + + setup { run("HISAT2_EXTRACTSPLICESITES") { script "../../../../modules/nf-core/hisat2/extractsplicesites/main.nf" diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap index 408dabff0..f5a872982 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap @@ -34,7 +34,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,845655ccfd1fd701b9f692f8db9508af" + "test.stats:md5,0ebab7bf6149e6378b263997d7073067" ] ], [ @@ -47,19 +47,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:06.813423" + "timestamp": "2024-09-16T08:27:35.808393107" }, "sarscov2 - bam - single_end - stub": { "content": [ @@ -134,12 +134,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -211,20 +211,20 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:23.861012" + "timestamp": "2024-09-16T08:10:09.451605417" }, "sarscov2 - bam - paired_end": { "content": [ @@ -261,7 +261,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,603fa8c9e0e9eb3769498fc989a29250" + "test.stats:md5,74b78cbd41df459e1037735f714cda4f" ] ], [ @@ -274,19 +274,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:25.071168" + "timestamp": "2024-09-16T08:28:01.671969576" }, "sarscov2 - bam - paired_end - stub": { "content": [ @@ -361,12 +361,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -438,19 +438,19 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:44.894976" + "timestamp": "2024-09-16T08:10:28.136547114" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 3fffd234b..352c62200 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -5,6 +5,8 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' + + test("test single end read with UMI") { when { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index 46bf3acf2..f8a746aa6 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -60,8 +60,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -122,17 +122,17 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:34.919444" + "timestamp": "2024-10-18T12:18:56.222595833" }, "test paired end read without UMI - stub": { "content": [ @@ -192,7 +192,7 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -250,16 +250,16 @@ ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:51.765414" + "timestamp": "2024-10-18T12:19:07.775855857" }, "test paired end read without UMI": { "content": [ @@ -288,15 +288,15 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:37.366404" + "timestamp": "2024-10-18T12:18:19.621101515" }, "test single end read with UMI": { "content": [ @@ -322,16 +322,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:04:53.072227" + "timestamp": "2024-10-18T12:17:51.049984482" }, "test paired end read with UMI": { "content": [ @@ -357,16 +357,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:16.709704" + "timestamp": "2024-10-18T12:18:07.106739839" }, "test skip all steps": { "content": [ @@ -447,8 +447,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -509,16 +509,16 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:09.844235" + "timestamp": "2024-10-18T12:18:42.513733457" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap index e0c944f31..d0509e559 100644 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap @@ -29,15 +29,15 @@ ] ], [ - "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c", + "versions.yml:md5,eb47b2c20a3565e58b613f66521da320" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:35.832206" + "timestamp": "2024-10-19T17:28:10.525956442" }, "homo_sapiens paired-end [fastq] - stub": { "content": [ @@ -103,8 +103,8 @@ ] ], "5": [ - "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c", + "versions.yml:md5,eb47b2c20a3565e58b613f66521da320" ], "index": [ [ @@ -167,15 +167,15 @@ ] ], "versions": [ - "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c", + "versions.yml:md5,eb47b2c20a3565e58b613f66521da320" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:56.819" + "timestamp": "2024-10-19T17:28:28.896824153" } } \ No newline at end of file diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test index d0a59629e..ce4ae964e 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test @@ -4,6 +4,8 @@ nextflow_workflow { script "../main.nf" workflow "QUANTIFY_PSEUDO_ALIGNMENT" + + test("salmon") { setup { diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap index 4db35cced..18a5eb761 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap @@ -54,17 +54,17 @@ ] ], [ - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", - "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" + "versions.yml:md5,efbc421f11a829423221fc2e67e03892" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:19.861809" + "timestamp": "2024-10-18T10:06:55.431718491" }, "salmon - stub": { "content": [ @@ -122,9 +122,9 @@ ] ], "14": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ], "2": [ @@ -308,18 +308,18 @@ ] ], "versions": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:55.281379" + "timestamp": "2024-10-18T10:07:30.425544183" }, "kallisto - stub": { "content": [ @@ -375,10 +375,10 @@ ] ], "14": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", - "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" + "versions.yml:md5,efbc421f11a829423221fc2e67e03892" ], "2": [ [ @@ -559,18 +559,18 @@ ] ], "versions": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", - "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" + "versions.yml:md5,efbc421f11a829423221fc2e67e03892" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:37:29.239014" + "timestamp": "2024-10-18T10:08:20.127524239" }, "salmon": { "content": [ @@ -629,16 +629,16 @@ ] ], [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:35:48.954002" + "timestamp": "2024-10-18T10:06:18.517305145" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432a..1638a410b 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "UTILS_NFSCHEMA_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/utils_nfschema_plugin" - tag "plugin/nf-schema" config "./nextflow.config" From 6739fbd5f6421000c7d51b6a3b320ec5d5ac0450 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 14:46:13 +0000 Subject: [PATCH 22/82] Update prepare_genome snaps --- .../prepare_genome/tests/main.nf.test.snap | 472 +++++++++--------- 1 file changed, 236 insertions(+), 236 deletions(-) diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap index 88d78c211..f5c0a10f7 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -41,17 +41,17 @@ "/ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/reference/transcriptome.fasta" ], [ - "versions.yml:md5,0bc25597acf1d50abf7070d19d311cd7", + "versions.yml:md5,4c712eb456b8ca2f6c237a981d6bd4f4", "versions.yml:md5,71252f1a221be05593361acccb99506b", - 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"versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T17:02:19.539518" + "timestamp": "2024-10-21T14:40:52.285127199" }, "skip_bbsplit - stub": { "content": [ @@ -2227,8 +2227,8 @@ "15": [ "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ], "2": [ "genome_transcriptome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -2302,15 +2302,15 @@ "versions": [ "versions.yml:md5,71252f1a221be05593361acccb99506b", "versions.yml:md5,80e9dd350be8cd4c11909d75c914757a", - "versions.yml:md5,bc99889446f02427c166b3219b793672", - "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa" + "versions.yml:md5,cc8f32b7c37c35a075d38cb773004eaa", + "versions.yml:md5,ccf59b1e546d2b873f052f6a2d8a0d1a" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:50:45.029123" + "timestamp": "2024-10-21T14:35:46.545484011" } } \ No newline at end of file From 75fad6fc261bce9c8ff1c07c55f521264bc3e877 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 14:58:14 +0000 Subject: [PATCH 23/82] Update align_star snaps --- .../local/align_star/tests/main.nf.test.snap | 89 +++++++++---------- 1 file changed, 40 insertions(+), 49 deletions(-) diff --git a/subworkflows/local/align_star/tests/main.nf.test.snap b/subworkflows/local/align_star/tests/main.nf.test.snap index e3a4b2e03..ec293ffd6 100644 --- a/subworkflows/local/align_star/tests/main.nf.test.snap +++ b/subworkflows/local/align_star/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "id": "test", "single_end": false }, - "test.bam.bai:md5,8bfbd4094a92ac0de8492d98a471d1b0" + "test.bam.bai:md5,4cf31974d82bed533f4b6528dff95b50" ] ], [ @@ -18,7 +18,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,fc154c31eb4d034ebdb6b1d17c6b45eb" + "test.bam:md5,7137528dd300c4ae0f7e3370a5555c79" ] ], [ @@ -81,7 +81,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,202e2f234f93b347b6a72d0163773054" + "test.stats:md5,bad7f610455554f5523eb1ae58ab7afe" ] ], [ @@ -94,19 +94,19 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666", + "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:13:41.194686" + "timestamp": "2024-10-21T14:53:32.322441137" }, "star - no igenomes - stub": { "content": [ @@ -134,10 +134,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -233,19 +230,19 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:43:30.675108" + "timestamp": "2024-10-21T14:53:57.659042129" }, "star - no igenomes": { "content": [ @@ -257,7 +254,7 @@ "id": "test", "single_end": false }, - "test.bam.bai:md5,8bfbd4094a92ac0de8492d98a471d1b0" + "test.bam.bai:md5,5b46703bf3e1294c8f0f98811bd661f9" ] ], [ @@ -266,17 +263,11 @@ "id": "test", "single_end": false }, - "test.bam:md5,e6573d093da6ec95f99c1669eb86bbd6" + "test.bam:md5,ac4e5cffcb5b580a119b1b03697f4621" ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] + ], [ @@ -329,7 +320,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,202e2f234f93b347b6a72d0163773054" + "test.stats:md5,bad7f610455554f5523eb1ae58ab7afe" ] ], [ @@ -342,19 +333,19 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T19:12:49.496188" + "timestamp": "2024-10-21T14:52:10.983503052" }, "star - with igenomes - stub": { "content": [ @@ -481,18 +472,18 @@ ] ], [ - "versions.yml:md5,06693106908e6f8f38a2c30accf7067d", - "versions.yml:md5,369619588c8c294b74dca9058a151b11", - "versions.yml:md5,78069d4515b04251f758ac52a49d9971", - "versions.yml:md5,b6a22ef369a375445a8f9313721b8092", - "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc", - "versions.yml:md5,feaf798d368c662a7a1cea87a24a7434" + "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", + "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", + "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", + "versions.yml:md5,d5e8b4d761dd85a303814239077bd666", + "versions.yml:md5,e3b043ba840d5bddde92f0bf1c91a5fc" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:43:56.680384" + "timestamp": "2024-10-21T14:54:32.959245404" } } \ No newline at end of file From a036f5d8f1e9e35cff9798d14a1e2fb2f91be519 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 14:58:35 +0000 Subject: [PATCH 24/82] Update quantify_rsem snaps --- .../quantify_rsem/tests/main.nf.test.snap | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap index 847be5d62..53368a78f 100644 --- a/subworkflows/local/quantify_rsem/tests/main.nf.test.snap +++ b/subworkflows/local/quantify_rsem/tests/main.nf.test.snap @@ -60,13 +60,13 @@ "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ], "17": [ + "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", + "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,3399809728955f4654ab781f37ea42d3", - "versions.yml:md5,4219f710ca21b71a7c7db6b02ac19bb3", - "versions.yml:md5,912c613bca84f899b3e890985ecc6fc2", - "versions.yml:md5,a4755dd9acbfa60dbc38e172ffda193f", + "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c", - "versions.yml:md5,f645ee5b20a4e89c6ed48fdc27c21791" + "versions.yml:md5,f151349bd7086cb08134496033e78cea", + "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" ], "2": [ [ @@ -258,21 +258,21 @@ ] ], "versions": [ + "versions.yml:md5,0f2bbea6c0412d2b185eab2dd0db06d5", + "versions.yml:md5,2a8e04c552c56aacc9a2d158fbc23a89", "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9", - "versions.yml:md5,3399809728955f4654ab781f37ea42d3", - "versions.yml:md5,4219f710ca21b71a7c7db6b02ac19bb3", - "versions.yml:md5,912c613bca84f899b3e890985ecc6fc2", - "versions.yml:md5,a4755dd9acbfa60dbc38e172ffda193f", + "versions.yml:md5,7696e625e0eda9d9ae30c8d5b3d23d9f", "versions.yml:md5,ae1676b60b6335fff8f1188288103a1c", - "versions.yml:md5,f645ee5b20a4e89c6ed48fdc27c21791" + "versions.yml:md5,f151349bd7086cb08134496033e78cea", + "versions.yml:md5,ff8adbe60177b3dba23d91b3424b10b6" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:32:06.579549" + "timestamp": "2024-10-21T14:49:44.270456428" }, "homo_sapiens": { "content": [ From 5dd65b92ffb68a6e42aba02d63a1ce8b0af1d88a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:11:37 +0000 Subject: [PATCH 25/82] [skip ci] First batch of pipeline test updates --- tests/default.nf.test.snap | 94 ++++++++++----------- tests/featurecounts_group_type.nf.test.snap | 74 ++++++++-------- tests/hisat2.nf.test.snap | 84 +++++++++--------- tests/kallisto.nf.test.snap | 46 +++++----- tests/min_mapped_reads.nf.test.snap | 86 +++++++++---------- 5 files changed, 192 insertions(+), 192 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ea663624c..204013425 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -4,16 +4,16 @@ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -36,8 +36,8 @@ "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -88,31 +88,31 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T09:21:27.152841" + "timestamp": "2024-10-21T15:18:53.239557126" }, "Params: default": { "content": [ 198, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -129,7 +129,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -174,22 +174,22 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" @@ -205,14 +205,14 @@ "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -221,7 +221,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1309,10 +1309,10 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", + "multiqc_featurecounts_biotype_plot.txt:md5,cdf1c096e3a9ecb0c1eecfd1f3b2e895", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1328,31 +1328,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1360,27 +1360,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", @@ -1392,21 +1392,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a8ad2573b09fbef181d2d5792a74dbd4", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", - "WT_REP1.biotype_counts_mqc.tsv:md5,cac41767a8cc2e5fee58637971ec89d1", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450", + "WT_REP1.biotype_counts_mqc.tsv:md5,e0dbe5dcff076b97775677fd64b29b04", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,112001ddbe917d935ee276d1685840bd", - "WT_REP2.biotype_counts_mqc.tsv:md5,e61b72317ac3c4d4ac64b663145e6262", + "WT_REP1.featureCounts.txt:md5,b2a80018f38c142a936e8ad5d24059f8", + "WT_REP2.biotype_counts_mqc.tsv:md5,5cb8f29f175d07b3d8f8464bf8fcd82b", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,59e23ae18cfe6aa2e5a884bc03cbff15", + "WT_REP2.featureCounts.txt:md5,0f3ed14df2ca681161c63aed8e6a7c7c", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -1457,8 +1457,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T09:48:14.477734" + "timestamp": "2024-10-21T15:17:50.647397994" } -} +} \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 9630b4c5d..b948e138d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -4,16 +4,16 @@ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -36,8 +36,8 @@ "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -88,31 +88,31 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:00:44.36432" + "timestamp": "2024-10-21T15:32:05.21244727" }, "Params: --featurecounts_group_type false": { "content": [ 188, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -129,7 +129,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -171,22 +171,22 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" @@ -202,11 +202,11 @@ "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -215,7 +215,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1275,7 +1275,7 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", @@ -1293,31 +1293,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1325,27 +1325,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", @@ -1407,8 +1407,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:00:00.235948" + "timestamp": "2024-10-21T15:31:07.10284645" } -} +} \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index f6fe94c7e..62e0b952f 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -4,16 +4,16 @@ 23, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -34,8 +34,8 @@ "hisat2": "2.2.1" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 @@ -89,31 +89,31 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:10:47.69497" + "timestamp": "2024-10-21T15:42:22.430556863" }, "Params: --aligner hisat2": { "content": [ 187, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -126,7 +126,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -178,35 +178,35 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -215,7 +215,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 @@ -1177,21 +1177,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9", "WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873", "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,079b099e5c5e9fe5e2559dfc938aa48b", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,cd7494b3bb12295a287f36506638f3c6", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,eedff929765dbc950528ee499e6d63ba", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,a60088d7013eebeb240e02457431eedb", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,4d1820a35481f454f17a14326356253d", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,b007abbc78b08d8d2bb37a267665947d", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,3e6a34d7435d5249229c849532a45930", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,3632da2126cb33391428ba0d6d10787f", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,ea897231d1c447d8e395716741b876ab", - "WT_REP1.biotype_counts_mqc.tsv:md5,abc303e93390bb5bd8f916f8f5978de3", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,72513319be04c591dcbbaf14f2081b32", + "WT_REP1.biotype_counts_mqc.tsv:md5,4b2f1b065666fbe235aa72ba06142025", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,39721c0d981304996438bc2f505bf98c", - "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794", + "WT_REP1.featureCounts.txt:md5,8faf3b2101c5e07bbf02415663855690", + "WT_REP2.biotype_counts_mqc.tsv:md5,994f8e87aeaa769479fcc4747ffbe6d9", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,702446d50a5019c84fcef85d1cfef78c", + "WT_REP2.featureCounts.txt:md5,efa5c0e711a3e0bdd42035be239e04a2", "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536", "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06", "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06", @@ -1256,10 +1256,10 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", + "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1275,31 +1275,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" @@ -1307,8 +1307,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T12:37:31.888584" + "timestamp": "2024-10-21T15:41:24.698018172" } -} +} \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 215a901a4..e48e6895f 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -4,22 +4,22 @@ 35, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -34,20 +34,20 @@ "gunzip": 1.1 }, "KALLISTO_INDEX": { - "kallisto": "0.48.0" + "kallisto": "0.51.1" }, "KALLISTO_QUANT": { - "kallisto": "0.48.0" + "kallisto": "0.51.1" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -245,31 +245,31 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-09T19:19:07.816437" + "timestamp": "2024-10-21T15:46:36.506804194" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ 17, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "GTF2BED": { "perl": "5.26.2" @@ -284,11 +284,11 @@ "gunzip": 1.1 }, "KALLISTO_INDEX": { - "kallisto": "0.48.0" + "kallisto": "0.51.1" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -327,8 +327,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-09T18:56:35.320816" + "timestamp": "2024-10-21T15:47:47.272256089" } -} +} \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index a494f6029..a66da2935 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -4,22 +4,22 @@ 152, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -81,22 +81,22 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" @@ -112,14 +112,14 @@ "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -128,7 +128,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1050,11 +1050,11 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", + "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1070,31 +1070,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1102,27 +1102,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", @@ -1130,15 +1130,15 @@ "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a8ad2573b09fbef181d2d5792a74dbd4", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -1173,25 +1173,25 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:36:48.24104" + "timestamp": "2024-10-21T15:58:09.750638828" }, "Params: --min_mapped_reads 90 - stub": { "content": [ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -1214,8 +1214,8 @@ "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1266,8 +1266,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T10:37:37.274627" + "timestamp": "2024-10-21T15:59:03.576783452" } -} +} \ No newline at end of file From 7568b2d180c07aa7b4e1f08aebc995e5dd4ecbff Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:17:42 +0000 Subject: [PATCH 26/82] [skip ci] Update subworkflow snaps due to patch on module --- .../tests/main.nf.test.snap | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 50ecf675d..092a78d6d 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - cram": { "content": [ "test.cram", - "test.cram.crai:md5,9a74bf028b7146d8ef285442a14bbc8f", + "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", "test.stats:md5,1a4569080c6f73546a863b0c3bc72c49", @@ -10,7 +10,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], @@ -18,7 +18,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T10:59:53.440891602" + "timestamp": "2024-10-21T16:16:11.433738207" }, "sarscov2 - bam - stub": { "content": [ @@ -90,7 +90,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -160,7 +160,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } @@ -169,7 +169,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T11:00:20.860494683" + "timestamp": "2024-10-21T16:16:33.62894627" }, "homo_sapiens - cram - stub": { "content": [ @@ -235,7 +235,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -299,7 +299,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } @@ -308,12 +308,12 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T11:00:42.042387118" + "timestamp": "2024-10-21T16:16:56.036736329" }, "sarscov2 - bam": { "content": [ - "test.bam:md5,c8a3a56d56bf2c87f09e143ed2f78a7d", - "test.bam.bai:md5,7d205e4e0b3d98887b1eafb5c50a3363", + "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b", + "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", "test.stats:md5,ba007b13981dad548358c7c957d41e12", @@ -321,7 +321,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,966dcea920866a87b55e665563864fc9", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], @@ -329,6 +329,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T10:59:22.840531827" + "timestamp": "2024-10-21T16:15:46.816427395" } } \ No newline at end of file From c3e0618613ea2ca962ffb1813ea3a58d54d0e86e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:21:07 +0000 Subject: [PATCH 27/82] [skip ci] bump remove_ribo_rna snaps --- tests/remove_ribo_rna.nf.test.snap | 94 +++++++++++++++--------------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index f10e886fe..308aaaa18 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -4,22 +4,22 @@ 205, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -81,22 +81,22 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" @@ -118,14 +118,14 @@ "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -134,7 +134,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1236,10 +1236,10 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", + "multiqc_featurecounts_biotype_plot.txt:md5,ea6aa981ce94cbcdcb6b2d593ac59157", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1255,31 +1255,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,306609f606004616a89ec50dc59f22b0", + "cmd_info.json:md5,3fa4eede50b6057d7ea52ca8aff1d641", "lib_format_counts.json:md5,b814fed52bd197a64544086dba0f127a", "ambig_info.tsv:md5,c83b0f9ebe9b8dfc284595ec56d4f092", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,6b367a9cdd2837b88890209459acf45f", + "cmd_info.json:md5,c5c31cc1202236ae2c800526c8a72827", "lib_format_counts.json:md5,3f4d67ace359562564dd336aa47a479c", "ambig_info.tsv:md5,00a1f9de7095a68dfb43e0a0301b6ecd", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c8c6208e1082ec150de56679b2b8cfe3", + "cmd_info.json:md5,e20c14f481b4468e11664f04ac06b166", "lib_format_counts.json:md5,f56087bcbd494c7fa78200f65a2400e2", "ambig_info.tsv:md5,54d942ddf69b4e8f1598064e09428256", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,5523405c02d30489d276e5d734cb54da", + "cmd_info.json:md5,8e239ec68573adbfcbcbac9238a1d433", "lib_format_counts.json:md5,43fc5463eada79e466d6ba9848739f06", "ambig_info.tsv:md5,933feffdaf6cf6ff407469ade0d7684d", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,998c89efb00fa5e63fd1d18c0602a019", + "cmd_info.json:md5,fa7b659f1ba90e16b0d0a375ff318b01", "lib_format_counts.json:md5,e6e3d7746e9abee6a0e097ae0ee1781a", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1287,27 +1287,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", @@ -1319,21 +1319,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f36792d25b268b6d556f8728300f4afc", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,accedae963f399d3b47effd8eda41edb", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c5865ded7168476d93057d2aedaec694", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,e37ededa12690a8ccae2eb42dac47ed6", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,782f5001d411ba79314ba77f7d36b157", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0fb30c2b937a5a41ac865ab09367af7", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,84cdcb79270d27007457fcaed5a1ad1b", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e", - "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,109c8988ccc98e6d2a45c3d55b07f2bd", + "WT_REP1.biotype_counts_mqc.tsv:md5,27ad551ae27516b73a113dcb3b944626", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05", - "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a", + "WT_REP1.featureCounts.txt:md5,5138add51ad34d3d4c525b0bf0f8bb1f", + "WT_REP2.biotype_counts_mqc.tsv:md5,e6bec82076f4cb2eff39f0d1bae70dc9", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a", + "WT_REP2.featureCounts.txt:md5,dd94f2f0c2ca58b9436429e33effd524", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -1384,25 +1384,25 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:03:32.596507" + "timestamp": "2024-10-21T16:16:27.003824312" }, "Params: --remove_ribo_rna - stub": { "content": [ 24, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -1428,8 +1428,8 @@ "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1480,8 +1480,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:04:25.816703" + "timestamp": "2024-10-21T16:17:20.86663416" } -} +} \ No newline at end of file From 206c792c8f633794f7008ad1aba38487be3e7b68 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:23:36 +0000 Subject: [PATCH 28/82] [skip ci] Update snaps for --pseudo_aligner salmon --skip_qc --skip_alignment --- tests/salmon.nf.test.snap | 50 +++++++++++++++++++-------------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 451c2918f..a83151bbb 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -4,22 +4,22 @@ 34, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -34,14 +34,14 @@ "gunzip": 1.1 }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -290,62 +290,62 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T07:25:22.063836" + "timestamp": "2024-10-21T16:22:14.604923669" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ 16, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "GTF2BED": { "perl": "5.26.2" @@ -360,8 +360,8 @@ "gunzip": 1.1 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -400,8 +400,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T07:07:48.845197" + "timestamp": "2024-10-21T16:23:12.380483903" } -} +} \ No newline at end of file From 9f9c8b1df64bac5edad9ae0017e03e19b868846a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:31:16 +0000 Subject: [PATCH 29/82] [skip ci] update star_rsem pipeline snaps --- tests/star_rsem.nf.test.snap | 84 ++++++++++++++++++------------------ 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 9d17e1f2d..a68d337c2 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -4,22 +4,22 @@ 188, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -88,35 +88,35 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -125,7 +125,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_RSEM_INDEX": { "untar": 1.34 @@ -1147,10 +1147,10 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", + "multiqc_featurecounts_biotype_plot.txt:md5,aef45c9c7814f3127cd3e9b77a5ed676", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1166,31 +1166,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1205,21 +1205,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e", "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965", "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,e66cd2b584d970ae3827ad2521f795ca", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,5a7a4291e8ff6cc25a4eb72dfdf06b51", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b3013c797d2fd38a8efa39047f5ba1b1", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,a8200ec76e7916dc1210447130f77bbf", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,548023e639f8eb76f973a2f98bcbc82c", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,ff59317794fc04d5a4fd18797f0ecb0f", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,577cd26ea14a25d5f667f05ef6d62816", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,2c0b5696582493f7a50259679982a6b3", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6ee84531ba255791a11b487b6aea75ab", - "WT_REP1.biotype_counts_mqc.tsv:md5,512645a8f736eee160c4465e1940f4a5", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,e405c75b21f6e8113ca8e114e9ae1f20", + "WT_REP1.biotype_counts_mqc.tsv:md5,d083ca421266ae2d4b3cd745b41ae110", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,289cc95971a3ec550e018659279c1f59", - "WT_REP2.biotype_counts_mqc.tsv:md5,d4957c0197636b68d27fbd60d388bba1", + "WT_REP1.featureCounts.txt:md5,32185355effd40ec8cdc1ee41dfd48ef", + "WT_REP2.biotype_counts_mqc.tsv:md5,c04c2936bbfac3bff284f96b7233b158", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,152d2f26df56a88fe4b27c742d8f7447", + "WT_REP2.featureCounts.txt:md5,04c506ad79af5295666847fa729e691c", "coverage_profile_along_genes_(high).txt:md5,31ab137e75752225365bd3d89143dbd2", "coverage_profile_along_genes_(low).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", "coverage_profile_along_genes_(total).txt:md5,eaceda909bf652b8301fa0ed1bba9ae1", @@ -1268,25 +1268,25 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T12:45:00.993602" + "timestamp": "2024-10-21T16:29:54.475156285" }, "Params: --aligner star_rsem - stub": { "content": [ 22, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "FASTQC": { "fastqc": "0.12.1" @@ -1304,8 +1304,8 @@ "gunzip": 1.1 }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_RSEM_INDEX": { "untar": 1.34 @@ -1359,8 +1359,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:41:09.240442" + "timestamp": "2024-10-21T16:31:04.240180676" } -} +} \ No newline at end of file From 102dc63a9eac719dfd76272d2aa3e5d539fd9a9e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:33:32 +0000 Subject: [PATCH 30/82] [skip ci] update pipeline tests for skip_qc --- tests/skip_qc.nf.test.snap | 74 +++++++++++++++++++------------------- 1 file changed, 37 insertions(+), 37 deletions(-) diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 476f26117..4c39ea615 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -4,16 +4,16 @@ 17, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { "python": null }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "GTF2BED": { "perl": "5.26.2" @@ -33,8 +33,8 @@ "gawk": "5.1.0" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -74,34 +74,34 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:17:30.991115" + "timestamp": "2024-10-21T16:32:13.845479978" }, "Params: --skip_qc": { "content": [ 136, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -119,22 +119,22 @@ "picard": "3.1.1" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" @@ -150,11 +150,11 @@ "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "TRIMGALORE": { - "trimgalore": "0.6.7", - "cutadapt": 3.4 + "trimgalore": "0.6.10", + "cutadapt": 4.2 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -163,7 +163,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -690,7 +690,7 @@ "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", - "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -703,58 +703,58 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", @@ -785,8 +785,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:16:41.081492" + "timestamp": "2024-10-21T16:31:26.493628799" } -} +} \ No newline at end of file From a9dc3ddd8bf8fbe73aaa7621fd497efdbe1d4a24 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:43:06 +0000 Subject: [PATCH 31/82] update skip_trimming snaps --- tests/skip_trimming.nf.test.snap | 72 ++++++++++++++++---------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 82acf3cfd..4ef81ceda 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -4,22 +4,22 @@ 193, { "BBMAP_BBSPLIT": { - "bbmap": 39.01 + "bbmap": 39.1 }, "BEDTOOLS_GENOMECOV_FW": { "bedtools": "2.31.1" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "CUSTOM_CATADDITIONALFASTA": { - "python": "3.9.5" + "python": "3.12.2" }, "CUSTOM_GETCHROMSIZES": { - "getchromsizes": 1.2 + "getchromsizes": 1.21 }, "CUSTOM_TX2GENE": { - "python": "3.9.5" + "python": "3.10.4" }, "DESEQ2_QC_PSEUDO": { "r-base": "4.0.3", @@ -36,7 +36,7 @@ "fastqc": "0.12.1" }, "FQ_SUBSAMPLE": { - "fq": "0.9.1 (2022-02-22)" + "fq": "0.12.0 (2024-07-08)" }, "GTF2BED": { "perl": "5.26.2" @@ -81,22 +81,22 @@ "rseqc": "5.0.2" }, "SALMON_QUANT": { - "salmon": "1.10.1" + "salmon": "1.10.3" }, "SAMTOOLS_FLAGSTAT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_SORT": { - "samtools": 1.2 + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": 1.2 + "samtools": 1.21 }, "SE_GENE": { "bioconductor-summarizedexperiment": "1.32.0" @@ -112,10 +112,10 @@ "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { - "stringtie": "2.2.1" + "stringtie": "2.2.3" }, "SUBREAD_FEATURECOUNTS": { - "subread": "2.0.1" + "subread": "2.0.6" }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -124,7 +124,7 @@ "ucsc": 377 }, "UCSC_BEDGRAPHTOBIGWIG": { - "ucsc": 445 + "ucsc": 469 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1110,7 +1110,7 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10", + "multiqc_featurecounts_biotype_plot.txt:md5,91d4ea5a6d4b02091be666eeab952443", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1126,31 +1126,31 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef", "lib_format_counts.json:md5,406e1457f0f0506bd8e605a217477436", "ambig_info.tsv:md5,0e0895adb376929bec8e0dd0677bf7d8", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3", "lib_format_counts.json:md5,afd2a0ddf0fd0ec4f99be898608a59db", "ambig_info.tsv:md5,6ed1b46c69917d6af3f093f9503bb962", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f", "lib_format_counts.json:md5,f7b7048fd2ac63fd792e71b85e4ed6d1", "ambig_info.tsv:md5,2f4c6a5953e41252a89851a9a7c36d9b", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4", "lib_format_counts.json:md5,03f0b70a4bb428fab96c29f04f895b6f", "ambig_info.tsv:md5,5fff63493bf3c223707ac90b9bb3a8f3", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4", "lib_format_counts.json:md5,4bf135c93c37f90c493f761f2709a28b", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", @@ -1158,27 +1158,27 @@ "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "cmd_info.json:md5,21395500c85658c70ce5fa0ac05b339a", "ambig_info.tsv:md5,452bbc83465339d2467663b061400b95", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "cmd_info.json:md5,faf70330c73fdce087631bb06de8a12f", "ambig_info.tsv:md5,f2aed38ba5251664024392bc89ae3f01", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "cmd_info.json:md5,563fd8191cc965524621c2afea7983ff", "ambig_info.tsv:md5,8d2b5ec0c441d9e078610480d179d116", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "cmd_info.json:md5,867de0b90aeccb5f9627e821a973aea7", "ambig_info.tsv:md5,44dad5d05b3c0c2ccb5a19a3a80333b3", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934", "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,fdeebc4f056cbb52fee53e82c2e0096f", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,aa94a148bdbebec4e82cd18a00316506", @@ -1190,21 +1190,21 @@ "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,147b051de3f1e5c75821176851d13612", "WT_REP1_intercept_slope.txt:md5,395cde13da1a90cf4378be2597c4f297", "WT_REP2_intercept_slope.txt:md5,7ddae43baa3c4e499fbc319b95627c41", - "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,27087a1c2e3cc2a0826818a04fe2647f", + "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,bc80cee5887507179965623c3dfef4f9", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", - "RAP1_IAA_30M_REP1.featureCounts.txt:md5,e8ec41e6e79f378e2f301e245a4f8e73", + "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b1ed22e51a94a0ca8f030ff4e09295aa", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,2e1d531352e9ad5935308e588dbaffe7", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", - "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,3afe2b0bcf265526c247016c32482314", + "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0ba869a8538e9bff9bf5976cdeecda6", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,6fedc1d11bc8d558f61c4c4a6060040f", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", - "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,6fed16d5ab57aa762891fde0c3720160", - "WT_REP1.biotype_counts_mqc.tsv:md5,ddcf909eacd91a49cc4fd3beed0b74f4", + "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,392538c1d377a72f6d89e5ace7e69bcd", + "WT_REP1.biotype_counts_mqc.tsv:md5,159e8125673fd75086d352ca1359d7b7", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,5155de67cf7537016c9ded607797f5c5", - "WT_REP2.biotype_counts_mqc.tsv:md5,d5d731cea7c5083a54069c1820101ba3", + "WT_REP1.featureCounts.txt:md5,f244c5de5ffa4afdf4d23becf4fa8c8d", + "WT_REP2.biotype_counts_mqc.tsv:md5,70bdca053da2f6f8a1aa29a5e32d2228", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", - "WT_REP2.featureCounts.txt:md5,94d2ccd74ec4338ddc8ad7bdbf297826", + "WT_REP2.featureCounts.txt:md5,24b7f969ede9c698de30aa0b3f881b8b", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,20c790387ef68e041bc4ffdcd032a22f", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,ba2636236fa1d26aa72f7aff73bd41f8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1c0458f66e4af56a56f4409c120434b3", @@ -1255,8 +1255,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-10T11:28:37.351353" + "timestamp": "2024-10-21T16:42:37.90820776" } } \ No newline at end of file From 787ab18a2c8e46fe760e5844bae497f3f18b41b7 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 16:45:31 +0000 Subject: [PATCH 32/82] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 07cc4de8d..8d453078a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes - [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release +- [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have arm builds ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From 13d384c1d5543c55656f577a36e248cb156255a2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 17:04:18 +0000 Subject: [PATCH 33/82] Revert hisat diff --- .../nf-core/hisat2/align/hisat2-align.diff | 22 +++++++------------ 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/hisat2/align/hisat2-align.diff b/modules/nf-core/hisat2/align/hisat2-align.diff index 216a70049..2a64e4f4f 100644 --- a/modules/nf-core/hisat2/align/hisat2-align.diff +++ b/modules/nf-core/hisat2/align/hisat2-align.diff @@ -1,7 +1,4 @@ Changes in module 'nf-core/hisat2/align' -'modules/nf-core/hisat2/align/environment.yml' is unchanged -'modules/nf-core/hisat2/align/meta.yml' is unchanged -Changes in 'hisat2/align/main.nf': --- modules/nf-core/hisat2/align/main.nf +++ modules/nf-core/hisat2/align/main.nf @@ -34,7 +34,7 @@ @@ -33,17 +30,6 @@ Changes in 'hisat2/align/main.nf': ${unaligned} -'modules/nf-core/hisat2/align/tests/main.nf.test.snap' is unchanged -Changes in 'hisat2/align/tests/tags.yml': ---- modules/nf-core/hisat2/align/tests/tags.yml -+++ modules/nf-core/hisat2/align/tests/tags.yml -@@ -1,4 +0,0 @@ --hisat2/align: -- - modules/nf-core/hisat2/align/** -- - modules/nf-core/hisat2/build/** -- - modules/nf-core/hisat2/extractsplicesites/** - -Changes in 'hisat2/align/tests/main.nf.test': --- modules/nf-core/hisat2/align/tests/main.nf.test +++ modules/nf-core/hisat2/align/tests/main.nf.test @@ -3,12 +3,6 @@ @@ -60,4 +46,12 @@ Changes in 'hisat2/align/tests/main.nf.test': test("Single-End") { +--- modules/nf-core/hisat2/align/tests/tags.yml ++++ /dev/null +@@ -1,4 +0,0 @@ +-hisat2/align: +- - modules/nf-core/hisat2/align/** +- - modules/nf-core/hisat2/build/** +- - modules/nf-core/hisat2/extractsplicesites/** + ************************************************************ From 9078e0f18f93149935531e4e5c02c21c7d120573 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 17:11:54 +0000 Subject: [PATCH 34/82] remove excess newlines --- modules/nf-core/bedtools/genomecov/tests/main.nf.test | 1 - modules/nf-core/custom/catadditionalfasta/tests/main.nf.test | 1 - modules/nf-core/custom/getchromsizes/tests/main.nf.test | 1 - modules/nf-core/custom/tx2gene/tests/main.nf.test | 1 - modules/nf-core/dupradar/tests/main.nf.test | 1 - modules/nf-core/fq/subsample/tests/main.nf.test | 1 - modules/nf-core/gffread/tests/main.nf.test | 1 - modules/nf-core/rseqc/inferexperiment/tests/main.nf.test | 1 - modules/nf-core/rseqc/innerdistance/tests/main.nf.test | 1 - modules/nf-core/rseqc/junctionannotation/tests/main.nf.test | 1 - modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test | 1 - modules/nf-core/samtools/stats/tests/main.nf.test | 1 - modules/nf-core/tximeta/tximport/tests/main.nf.test | 1 - modules/nf-core/umitools/dedup/tests/main.nf.test | 1 - modules/nf-core/umitools/prepareforrsem/tests/main.nf.test | 1 - .../nf-core/bam_markduplicates_picard/tests/main.nf.test | 1 - .../nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test | 2 -- .../nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test | 1 - .../nf-core/quantify_pseudo_alignment/tests/main.nf.test | 1 - 19 files changed, 20 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test index 13f043102..b8caa1e11 100644 --- a/modules/nf-core/bedtools/genomecov/tests/main.nf.test +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { process "BEDTOOLS_GENOMECOV" config "./nextflow.config" - test("sarscov2 - no scale") { when { process { diff --git a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test index f13f39fa4..878c05d16 100644 --- a/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test +++ b/modules/nf-core/custom/catadditionalfasta/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_CATADDITIONALFASTA" - test("sarscov2 - fastq - gtf") { when { diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test b/modules/nf-core/custom/getchromsizes/tests/main.nf.test index 8a05aeaae..2dadc1a55 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_GETCHROMSIZES" - test("test_custom_getchromsizes") { when { diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index 2d45b7646..e56a0b8fe 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "CUSTOM_TX2GENE" - test("saccharomyces_cerevisiae - gtf") { setup { diff --git a/modules/nf-core/dupradar/tests/main.nf.test b/modules/nf-core/dupradar/tests/main.nf.test index d45cefcfe..60f8dfb7d 100644 --- a/modules/nf-core/dupradar/tests/main.nf.test +++ b/modules/nf-core/dupradar/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "DUPRADAR" - test("sarscov2 - bam - single_end") { config './nextflow.config' diff --git a/modules/nf-core/fq/subsample/tests/main.nf.test b/modules/nf-core/fq/subsample/tests/main.nf.test index a7880501b..13bb75945 100644 --- a/modules/nf-core/fq/subsample/tests/main.nf.test +++ b/modules/nf-core/fq/subsample/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "FQ_SUBSAMPLE" - test("test_fq_subsample_no_args") { config "./nextflow_no_args.config" when { diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index 6d7c063ef..e03820f4d 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "GFFREAD" - test("sarscov2-gff3-gtf") { config "./nextflow.config" diff --git a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test index 37eb8b1f5..375f65357 100644 --- a/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test +++ b/modules/nf-core/rseqc/inferexperiment/tests/main.nf.test @@ -5,7 +5,6 @@ nextflow_process { process "RSEQC_INFEREXPERIMENT" config "./nextflow.config" - test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test index 633d27d12..e54036f8a 100644 --- a/modules/nf-core/rseqc/innerdistance/tests/main.nf.test +++ b/modules/nf-core/rseqc/innerdistance/tests/main.nf.test @@ -5,7 +5,6 @@ nextflow_process { process "RSEQC_INNERDISTANCE" config "./nextflow.config" - test("sarscov2 - [[meta] - bam] - bed") { when { diff --git a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test index b0e4eb86c..8a05bccab 100644 --- a/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionannotation/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONANNOTATION" - test("sarscov2 - paired end [bam]") { when { diff --git a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test index 311125576..69d7f0c5d 100644 --- a/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test +++ b/modules/nf-core/rseqc/junctionsaturation/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "RSEQC_JUNCTIONSATURATION" - test("sarscov2 paired-end [bam]") { when { diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index ea8a233de..6416ae127 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "SAMTOOLS_STATS" - test("bam") { when { diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test index d26e54100..782030fb8 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "TXIMETA_TXIMPORT" - test("saccharomyces_cerevisiae - kallisto - gtf") { setup { diff --git a/modules/nf-core/umitools/dedup/tests/main.nf.test b/modules/nf-core/umitools/dedup/tests/main.nf.test index 4ba50c5fe..883e2d9d7 100644 --- a/modules/nf-core/umitools/dedup/tests/main.nf.test +++ b/modules/nf-core/umitools/dedup/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_DEDUP" - test("se - no stats") { config "./nextflow.config" diff --git a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test index 4dfb522a3..105093505 100644 --- a/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test +++ b/modules/nf-core/umitools/prepareforrsem/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_process { script "../main.nf" process "UMITOOLS_PREPAREFORRSEM" - test("sarscov2 - bam") { when { diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test index 48dbcf2f0..f023a9f7d 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -4,7 +4,6 @@ nextflow_workflow { script "../main.nf" workflow "BAM_MARKDUPLICATES_PICARD" - test("sarscov2 - bam") { when { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test index eb944b7d5..053feffb6 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test @@ -181,7 +181,6 @@ nextflow_workflow { } } - test("skip_umi_extract") { when { @@ -675,7 +674,6 @@ nextflow_workflow { } } - test("skip_umi_extract - stub") { options "-stub" diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 352c62200..1043d06ad 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -6,7 +6,6 @@ nextflow_workflow { config './nextflow.config' - test("test single end read with UMI") { when { diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test index ce4ae964e..9c484b4aa 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test @@ -5,7 +5,6 @@ nextflow_workflow { workflow "QUANTIFY_PSEUDO_ALIGNMENT" - test("salmon") { setup { From a7983ec3c2551c93b8e1b5c02be9575ca959435f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 18:31:27 +0000 Subject: [PATCH 35/82] Bump star modules --- modules.json | 4 +- modules/nf-core/star/align/environment.yml | 6 +- modules/nf-core/star/align/main.nf | 4 +- modules/nf-core/star/align/tests/main.nf.test | 36 +--- .../star/align/tests/main.nf.test.snap | 190 ++++-------------- .../star/genomegenerate/environment.yml | 6 +- modules/nf-core/star/genomegenerate/main.nf | 4 +- .../genomegenerate/tests/main.nf.test.snap | 28 +-- 8 files changed, 80 insertions(+), 198 deletions(-) diff --git a/modules.json b/modules.json index c64fdaea8..7bea6205b 100644 --- a/modules.json +++ b/modules.json @@ -219,12 +219,12 @@ }, "star/align": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", "installed_by": ["modules"] }, "stringtie/stringtie": { diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 1debc4c9b..7c57530a3 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -3,7 +3,7 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.18 - - bioconda::samtools=1.18 - - bioconda::star=2.7.10a + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 + - bioconda::star=2.7.11b - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index b5bc9ddf8..417071ba9 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,8 +4,8 @@ process STAR_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : + 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 69f655ef4..2fa21352e 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -51,13 +51,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -119,13 +116,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -187,13 +181,9 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -255,13 +245,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + file(process.out.junction[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -325,13 +312,10 @@ nextflow_process { file(process.out.log_final[0][1]).name, file(process.out.log_out[0][1]).name, file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), process.out.bedgraph, process.out.fastq, - process.out.junction, process.out.read_per_gene_tab, process.out.sam, process.out.spl_junc_tab, @@ -601,4 +585,4 @@ nextflow_process { ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index 0da28d37c..b533fb8b4 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -97,7 +97,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -307,7 +307,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -322,9 +322,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:39:15.440397" + "timestamp": "2024-10-20T17:09:08.738074176" }, "homo_sapiens - paired_end - arriba - stub": { "content": [ @@ -424,7 +424,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -634,7 +634,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -649,33 +649,17 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:40:15.472109" + "timestamp": "2024-10-20T17:09:36.122131869" }, "homo_sapiens - single_end": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535" - ] - ], - [ - - ], - [ - - ], - [ - - ], + "9f76be49a6607613a64f760101bdddce", + "9f76be49a6607613a64f760101bdddce", [ [ { @@ -696,9 +680,6 @@ ], [ - ], - [ - ], [ [ @@ -722,38 +703,22 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:23:08.001162" + "timestamp": "2024-10-20T17:01:22.197991909" }, "homo_sapiens - paired_end": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] - ], - [ - - ], - [ - - ], - [ - - ], + "db9a8324b5163b025bcc0c33e848486", + "db9a8324b5163b025bcc0c33e848486", [ [ { @@ -774,9 +739,6 @@ ], [ - ], - [ - ], [ [ @@ -800,14 +762,14 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:24:46.295219" + "timestamp": "2024-10-20T17:02:06.988663857" }, "homo_sapiens - paired_end - multiple - stub": { "content": [ @@ -907,7 +869,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -1117,7 +1079,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -1132,33 +1094,17 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:41:07.310866" + "timestamp": "2024-10-20T17:10:12.005468781" }, "homo_sapiens - paired_end - multiple": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" - ] - ], - [ - - ], - [ - - ], - [ - - ], + "3e54e45f5dc3e9c1f2fc55bc41531a87", + "3e54e45f5dc3e9c1f2fc55bc41531a87", [ [ { @@ -1179,9 +1125,6 @@ ], [ - ], - [ - ], [ [ @@ -1205,14 +1148,14 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:38:46.605044" + "timestamp": "2024-10-20T17:08:54.877286681" }, "homo_sapiens - paired_end - stub": { "content": [ @@ -1312,7 +1255,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -1522,7 +1465,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -1537,24 +1480,17 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:39:51.595873" + "timestamp": "2024-10-20T17:09:20.911466345" }, "homo_sapiens - paired_end - starfusion": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.out.bam:md5,bcad07b838f6762fc01eea52b5cd3f84" - ] - ], + "test.Chimeric.out.junction", + "caee9dcda13882d4913456973c25b57a", [ ], @@ -1566,24 +1502,6 @@ ], [ - ], - [ - - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Chimeric.out.junction:md5,c10ef219f4a30e83711b995bc5e40dba" - ] - ], - [ - - ], - [ - ], [ [ @@ -1607,41 +1525,21 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:35:43.874508" + "timestamp": "2024-10-20T17:07:25.0639914" }, "homo_sapiens - paired_end - arriba": { "content": [ "test.Log.final.out", "test.Log.out", "test.Log.progress.out", - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5" - ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], + "1a3abe88fb2490589c58497d39921bcc", [ ], @@ -1676,14 +1574,14 @@ ], [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:28:32.599223" + "timestamp": "2024-10-20T17:04:00.685784211" }, "homo_sapiens - paired_end - starfusion - stub": { "content": [ @@ -1783,7 +1681,7 @@ ] ], "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "4": [ [ @@ -1993,7 +1891,7 @@ ] ], "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + "versions.yml:md5,a149bba1dbb5194560abdd813c7848e3" ], "wig": [ [ @@ -2008,8 +1906,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-01T11:40:42.29249" + "timestamp": "2024-10-20T17:09:53.173671551" } } \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 1debc4c9b..7c57530a3 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -3,7 +3,7 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.18 - - bioconda::samtools=1.18 - - bioconda::star=2.7.10a + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 + - bioconda::star=2.7.11b - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index b8855715b..8f0c67e76 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -4,8 +4,8 @@ process STAR_GENOMEGENERATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : + 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 207f4b4f5..3db256782 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]", [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:55:35.478401" + "timestamp": "2024-10-19T20:37:47.410432728" }, "fasta_gtf_stub": { "content": [ @@ -41,7 +41,7 @@ ] ], "1": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ], "index": [ [ @@ -69,15 +69,15 @@ ] ], "versions": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:55:57.247585" + "timestamp": "2024-10-19T20:38:09.165234795" }, "fasta_stub": { "content": [ @@ -101,7 +101,7 @@ ] ], "1": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ], "index": [ [ @@ -122,27 +122,27 @@ ] ], "versions": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:56:07.01742" + "timestamp": "2024-10-19T20:38:19.530862664" }, "fasta": { "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]", [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,14b05d04c9eca568e9ed4888aaf26fa6" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:55:45.48784" + "timestamp": "2024-10-19T20:37:58.667436398" } } \ No newline at end of file From f99460d1c0263d8cab75d8a74053458f7b5ff2b5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 20:38:52 +0000 Subject: [PATCH 36/82] Update option for new STAR --- subworkflows/local/align_star/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 511ff6e63..3d07c9e88 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -20,7 +20,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD - --quantTranscriptomeBan Singleend + --quantTranscriptomeSAMoutput BanSingleEnd --outSAMstrandField intronMotif ${params.save_unaligned || params.contaminant_screening ? '--outReadsUnmapped Fastx' : ''} """.trim()) From ce7486b5ebbc37cda8558ae3e2d51e772897773d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 20:39:01 +0000 Subject: [PATCH 37/82] Fix up pipeline tests --- tests/default.nf.test.snap | 44 ++++++++++----------- tests/featurecounts_group_type.nf.test.snap | 38 +++++++++--------- tests/min_mapped_reads.nf.test.snap | 20 +++++----- tests/remove_ribo_rna.nf.test.snap | 44 ++++++++++----------- tests/skip_qc.nf.test.snap | 22 +++++------ tests/skip_trimming.nf.test.snap | 10 ++--- 6 files changed, 89 insertions(+), 89 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 204013425..d50bdafc0 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -31,8 +31,8 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:18:53.239557126" + "timestamp": "2024-10-21T18:47:30.454374101" }, "Params: default": { "content": [ @@ -195,13 +195,13 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { @@ -1312,18 +1312,18 @@ "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,cdf1c096e3a9ecb0c1eecfd1f3b2e895", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", + "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", + "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1385,12 +1385,12 @@ "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", + "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", + "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", @@ -1401,9 +1401,9 @@ "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450", - "WT_REP1.biotype_counts_mqc.tsv:md5,e0dbe5dcff076b97775677fd64b29b04", + "WT_REP1.biotype_counts_mqc.tsv:md5,3d9d1dca4551ff5689f36ba3f23848f2", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,b2a80018f38c142a936e8ad5d24059f8", + "WT_REP1.featureCounts.txt:md5,e64f59d719d21293627717beb76beaf5", "WT_REP2.biotype_counts_mqc.tsv:md5,5cb8f29f175d07b3d8f8464bf8fcd82b", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,0f3ed14df2ca681161c63aed8e6a7c7c", @@ -1421,9 +1421,9 @@ "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", - "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(high).txt:md5,3863e6277dc95e3fac3f9cd5095a08eb", + "coverage_profile_along_genes_(low).txt:md5,df84b2f592a0f02310096a2dd053397d", + "coverage_profile_along_genes_(total).txt:md5,df84b2f592a0f02310096a2dd053397d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1445,7 +1445,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -1459,6 +1459,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:17:50.647397994" + "timestamp": "2024-10-21T19:14:46.845308285" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index b948e138d..d72672710 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -31,8 +31,8 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:32:05.21244727" + "timestamp": "2024-10-21T18:52:01.516368536" }, "Params: --featurecounts_group_type false": { "content": [ @@ -192,13 +192,13 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { @@ -1278,17 +1278,17 @@ "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", - "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", + "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", + "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1350,12 +1350,12 @@ "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", - "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", + "WT_REP1_dupMatrix.txt:md5,faaa9a4d73efb7188bbe4a480c680ea0", "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", - "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", + "WT_REP1_intercept_slope.txt:md5,051e7b02c31dd614d580d8b44e1b6898", "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", @@ -1371,9 +1371,9 @@ "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", - "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(high).txt:md5,3863e6277dc95e3fac3f9cd5095a08eb", + "coverage_profile_along_genes_(low).txt:md5,df84b2f592a0f02310096a2dd053397d", + "coverage_profile_along_genes_(total).txt:md5,df84b2f592a0f02310096a2dd053397d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", @@ -1395,7 +1395,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -1409,6 +1409,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:31:07.10284645" + "timestamp": "2024-10-21T19:24:36.371474446" } } \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index a66da2935..2f4db1480 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -102,13 +102,13 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { @@ -1055,7 +1055,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1065,7 +1065,7 @@ "rseqc_infer_experiment_plot.txt:md5,749a802379ada3ec9d2083ecbe6aef7e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1175,7 +1175,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:58:09.750638828" + "timestamp": "2024-10-21T19:45:32.241828903" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1209,8 +1209,8 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { @@ -1268,6 +1268,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:59:03.576783452" + "timestamp": "2024-10-21T19:46:21.485818867" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 308aaaa18..8dedc7693 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -108,13 +108,13 @@ "sortmerna": "4.3.6" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { @@ -1239,18 +1239,18 @@ "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_featurecounts_biotype_plot.txt:md5,ea6aa981ce94cbcdcb6b2d593ac59157", - "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", + "multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba", + "multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_gene_coverage_profile_Counts.txt:md5,50e9209baeaafe181ce3b5caa05cf789", - "qualimap_gene_coverage_profile_Normalised.txt:md5,6ed32f112c679e73396350cbe5cb9459", - "qualimap_rnaseq_cov_hist.txt:md5,a895b3af229f661da1edbc21ec72edaa", + "qualimap_gene_coverage_profile_Counts.txt:md5,286d47f67e1d034a88e122091ae30f3d", + "qualimap_gene_coverage_profile_Normalised.txt:md5,3297068282f57506f40070b8bc6ad1b5", + "qualimap_rnaseq_cov_hist.txt:md5,a523cfcb52fe8f2d5902d933568a790d", "rseqc_infer_experiment_plot.txt:md5,d8741451248f1a5a4ebe3230c1af9c95", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,4ff26c0457ddceb4a03e874222b46f00", "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -1312,12 +1312,12 @@ "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,ddadea4a08511aae6faeb632eb6aafea", "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,1db4c86723cf69052c4386760a9750bb", "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,c0bf1135d2d70c5918d87f706c0c54bc", - "WT_REP1_dupMatrix.txt:md5,b0de1683f2a9bfa42437e924a11648fd", + "WT_REP1_dupMatrix.txt:md5,b82c4fed335d03e85c414c91c2efd461", "WT_REP2_dupMatrix.txt:md5,bab18079153627205e5d907d8dfba677", "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,b21a53b0156b0afdfc28c237cb11218d", "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,eccc5ca37855c717d35477e684188695", "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,c3900f3bb24cd339d0e0ecf65ae43217", - "WT_REP1_intercept_slope.txt:md5,f38c8525b7fcb990b7158f1518e451ad", + "WT_REP1_intercept_slope.txt:md5,7db7a898152e8eaab96b1aaf0e567e50", "WT_REP2_intercept_slope.txt:md5,9bcbc18d0d331fe3c972538456ffd5b2", "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,accedae963f399d3b47effd8eda41edb", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", @@ -1328,9 +1328,9 @@ "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,109c8988ccc98e6d2a45c3d55b07f2bd", - "WT_REP1.biotype_counts_mqc.tsv:md5,27ad551ae27516b73a113dcb3b944626", + "WT_REP1.biotype_counts_mqc.tsv:md5,97caee79e83b5fce6e5504c0daefe474", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", - "WT_REP1.featureCounts.txt:md5,5138add51ad34d3d4c525b0bf0f8bb1f", + "WT_REP1.featureCounts.txt:md5,2d37cf435f77164dc9dfd11725b60528", "WT_REP2.biotype_counts_mqc.tsv:md5,e6bec82076f4cb2eff39f0d1bae70dc9", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,dd94f2f0c2ca58b9436429e33effd524", @@ -1348,9 +1348,9 @@ "coverage_profile_along_genes_(high).txt:md5,634f447f91db940d2148af74cf36febd", "coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", - "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc", + "coverage_profile_along_genes_(high).txt:md5,40b488dc478b4bf6d802319e89846c0a", + "coverage_profile_along_genes_(low).txt:md5,9f1e68e98d4d663aac436305c99cceaf", + "coverage_profile_along_genes_(total).txt:md5,9f1e68e98d4d663aac436305c99cceaf", "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", @@ -1372,7 +1372,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,682817a9d0a1ac9c1637249e007d3514", + "e_data.ctab:md5,68812b283993f721b237ae6cdecc30d5", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -1386,7 +1386,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:16:27.003824312" + "timestamp": "2024-10-21T20:02:26.804814864" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1423,8 +1423,8 @@ "sortmerna": "4.3.6" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { @@ -1482,6 +1482,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:17:20.86663416" + "timestamp": "2024-10-21T20:03:16.221160765" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 4c39ea615..cb94364bb 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -28,8 +28,8 @@ "gunzip": 1.1 }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "TRIMGALORE": { @@ -76,7 +76,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:32:13.845479978" + "timestamp": "2024-10-21T20:14:28.433411196" }, "Params: --skip_qc": { "content": [ @@ -140,13 +140,13 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { @@ -692,13 +692,13 @@ "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", - "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -773,7 +773,7 @@ "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", - "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", + "e_data.ctab:md5,7cc6dedfc89b50e4be8c3ba82ba4f8aa", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", @@ -787,6 +787,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:31:26.493628799" + "timestamp": "2024-10-21T20:13:44.078197492" } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 4ef81ceda..56f9b6eba 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -102,13 +102,13 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STAR_GENOMEGENERATE": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.2, "gawk": "5.1.0" }, "STRINGTIE_STRINGTIE": { @@ -1257,6 +1257,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:42:37.90820776" + "timestamp": "2024-10-21T20:23:07.88998048" } } \ No newline at end of file From 7116a9a641f6f08480202dc72e4be098dfea062a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 20:44:19 +0000 Subject: [PATCH 38/82] Fix local star swf to match star --- .../local/align_star/tests/main.nf.test.snap | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/align_star/tests/main.nf.test.snap b/subworkflows/local/align_star/tests/main.nf.test.snap index ec293ffd6..b8224b7fd 100644 --- a/subworkflows/local/align_star/tests/main.nf.test.snap +++ b/subworkflows/local/align_star/tests/main.nf.test.snap @@ -230,8 +230,8 @@ ] ], [ - "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634", "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,708098dd31c984730b066ead621a33f7", "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", @@ -242,7 +242,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T14:53:57.659042129" + "timestamp": "2024-10-21T20:42:29.835710637" }, "star - no igenomes": { "content": [ @@ -254,7 +254,7 @@ "id": "test", "single_end": false }, - "test.bam.bai:md5,5b46703bf3e1294c8f0f98811bd661f9" + "test.bam.bai:md5,59e8552f0e50c540d41198496bf34251" ] ], [ @@ -263,7 +263,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,ac4e5cffcb5b580a119b1b03697f4621" + "test.bam:md5,0d47a5f971c1548eadc1f3c39dab0dbf" ] ], [ @@ -311,7 +311,7 @@ "id": "test", "single_end": false }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" + "test.Aligned.sortedByCoord.out.bam:md5,4e917b4befbbe216fd666d06af0298af" ] ], [ @@ -333,8 +333,8 @@ ] ], [ - "versions.yml:md5,35c1cc21d26d9d8f00e6ec87e97fb634", "versions.yml:md5,5ad5e88ee4e52ccabeef61dcd368d30b", + "versions.yml:md5,708098dd31c984730b066ead621a33f7", "versions.yml:md5,92f25606f0ee994dac8c00fe49676e5a", "versions.yml:md5,9611f602102b5aed0fe2b947f9d2270c", "versions.yml:md5,b92d6ad60847882b0089f551c5cfc366", @@ -345,7 +345,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T14:52:10.983503052" + "timestamp": "2024-10-21T20:40:55.299198285" }, "star - with igenomes - stub": { "content": [ From 5cb8974cbe1d3c7331aedfbd1115da0a50a1bc91 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 21 Oct 2024 20:45:40 +0000 Subject: [PATCH 39/82] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8d453078a..0eb8458bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Enhancements & fixes - [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release -- [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have arm builds +- [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds +- [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From 1b8efca194a5808dddc1b7208c3b74dd16ec27a9 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 11:33:52 +0000 Subject: [PATCH 40/82] patch sortmerna to 4.3.7 in seqera channel pending a functional verison appearing in conda-forge --- modules.json | 3 +- modules/nf-core/sortmerna/environment.yml | 2 +- modules/nf-core/sortmerna/main.nf | 4 +- modules/nf-core/sortmerna/sortmerna.diff | 539 ++++++++++++++++++ modules/nf-core/sortmerna/tests/main.nf.test | 15 +- .../nf-core/sortmerna/tests/main.nf.test.snap | 251 ++++---- 6 files changed, 659 insertions(+), 155 deletions(-) create mode 100644 modules/nf-core/sortmerna/sortmerna.diff diff --git a/modules.json b/modules.json index 7bea6205b..7f889aeec 100644 --- a/modules.json +++ b/modules.json @@ -215,7 +215,8 @@ "sortmerna": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"], + "patch": "modules/nf-core/sortmerna/sortmerna.diff" }, "star/align": { "branch": "master", diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index fab44081f..75d586704 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sortmerna=4.3.6 + - seqera::sortmerna=4.3.7 diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 7c17e500c..6850dc1d7 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -4,8 +4,8 @@ process SORTMERNA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : - 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : + 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sortmerna/sortmerna.diff b/modules/nf-core/sortmerna/sortmerna.diff new file mode 100644 index 000000000..5c3b1775d --- /dev/null +++ b/modules/nf-core/sortmerna/sortmerna.diff @@ -0,0 +1,539 @@ +Changes in module 'nf-core/sortmerna' +Changes in 'sortmerna/main.nf': +--- modules/nf-core/sortmerna/main.nf ++++ modules/nf-core/sortmerna/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : +- 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : ++ 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' }" + + input: + tuple val(meta), path(reads) + +Changes in 'sortmerna/environment.yml': +--- modules/nf-core/sortmerna/environment.yml ++++ modules/nf-core/sortmerna/environment.yml +@@ -2,4 +2,4 @@ + - conda-forge + - bioconda + dependencies: +- - bioconda::sortmerna=4.3.6 ++ - seqera::sortmerna=4.3.7 + +'modules/nf-core/sortmerna/meta.yml' is unchanged +'modules/nf-core/sortmerna/nextflow.config' was created +Changes in 'sortmerna/tests/main.nf.test.snap': +--- modules/nf-core/sortmerna/tests/main.nf.test.snap ++++ modules/nf-core/sortmerna/tests/main.nf.test.snap +@@ -2,14 +2,14 @@ + "versions_paired_end_stub": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:27:11.223149" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:01.533875274" + }, + "index_paired_end_stub": { + "content": [ +@@ -25,48 +25,22 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:24:25.384097178" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:01.450465678" + }, + "versions_paired_end": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:27:04.517155" +- }, +- "versions_single_end_stub": { +- "content": [ +- [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-01T12:10:35.228450189" +- }, +- "sarscov2 single_end_match": { +- "content": [ +- [ +- "test.non_rRNA.fastq.gz", +- "test.sortmerna.log", +- "{id=test}" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:23.20327" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:48.811712136" + }, + "index_only_stub": { + "content": [ +@@ -82,44 +56,79 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:47.128504164" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:38:56.554562414" ++ }, ++ "sarscov2 single_end_match": { ++ "content": [ ++ [ ++ "test.non_rRNA.fastq.gz", ++ "test.sortmerna.log", ++ "{id=test}" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:09.015863183" ++ }, ++ "versions_single_end_stub": { ++ "content": [ ++ [ ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:28.573618474" + }, + "index_single_end_premade_index": { + "content": [ + [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:01:53.832643452" ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:14.159307146" + }, + "versions_single_end_premade_index": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:01:53.902154982" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:14.269803641" ++ }, ++ "sarscov2 indexing only": { ++ "content": [ ++ [ ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ ], ++ [ ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:38:39.794977786" + }, + "sarscov2 paired_end-for_stub_match": { + "content": [ +@@ -133,32 +142,24 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:56.063579" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:01.365507281" + }, + "index_paired_end": { + "content": [ + [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:24:14.272659781" ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:48.72523749" + }, + "sarscov2 single_end_premade_index_match_stub": { + "content": [ +@@ -169,10 +170,10 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:05:01.913287272" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:28.87594616" + }, + "sarscov2 single_end-for_stub_match": { + "content": [ +@@ -183,10 +184,10 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:29.197913" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:28.458349619" + }, + "sarscov2 paired_end_match": { + "content": [ +@@ -200,46 +201,46 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-07T12:28:49.914992" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:48.667990373" + }, + "versions_single_end": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:36:27.14244294" +- }, +- "versions_index_only": { +- "content": [ +- [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:35.609161481" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:09.110655329" + }, + "versions_single_end_premade_index_stub": { + "content": [ + [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:05:02.059858431" ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:29.097777821" ++ }, ++ "versions_index_only_stub": { ++ "content": [ ++ [ ++ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:38:56.592840673" + }, + "index_single_end_stub": { + "content": [ +@@ -255,22 +256,10 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:23:58.068772508" +- }, +- "versions_index_only_stub": { +- "content": [ +- [ +- "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:47.169402699" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:28.516407836" + }, + "index_single_end_premade_index_stub": { + "content": [ +@@ -286,54 +275,24 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:05:01.953316205" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:28.988436085" + }, + "index_single_end": { + "content": [ + [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T14:36:26.88061978" +- }, +- "index_index_only": { +- "content": [ +- [ +- [ +- { +- "id": "test2" +- }, +- [ +- "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", +- "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", +- "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", +- "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" +- ] +- ] +- ] +- ], +- "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:00:35.34089252" ++ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ ] ++ ], ++ "meta": { ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:39:09.050777261" + }, + "sarscov2 single_end_premade_index_match": { + "content": [ +@@ -344,9 +303,9 @@ + ] + ], + "meta": { +- "nf-test": "0.8.4", +- "nextflow": "23.10.1" +- }, +- "timestamp": "2024-02-26T15:01:53.797737296" ++ "nf-test": "0.9.0", ++ "nextflow": "24.04.4" ++ }, ++ "timestamp": "2024-10-22T10:40:14.075100849" + } + } +Changes in 'sortmerna/tests/main.nf.test': +--- modules/nf-core/sortmerna/tests/main.nf.test ++++ modules/nf-core/sortmerna/tests/main.nf.test +@@ -27,8 +27,10 @@ + assertAll( + { assert process.success }, + { assert ! process.out.reads }, +- { assert snapshot(process.out.index).match("index_index_only") }, +- { assert snapshot(process.out.versions).match("versions_index_only") } ++ { assert snapshot( ++ file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }, ++ process.out.versions ++ ).match() }, + ) + } + +@@ -92,7 +94,7 @@ + ).sort() + ).match("sarscov2 single_end_match") + }, +- { assert snapshot(process.out.index).match("index_single_end") }, ++ { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_single_end") }, + { assert snapshot(process.out.versions).match("versions_single_end") } + ) + } +@@ -170,7 +172,7 @@ + ).sort() + ).match("sarscov2 paired_end_match") + }, +- { assert snapshot(process.out.index).match("index_paired_end") }, ++ { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_paired_end") }, + { assert snapshot(process.out.versions).match("versions_paired_end") } + ) + } +@@ -265,7 +267,7 @@ + ).sort() + ).match("sarscov2 single_end_premade_index_match") + }, +- { assert snapshot(process.out.index).match("index_single_end_premade_index") }, ++ { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }).match("index_single_end_premade_index") }, + { assert snapshot(process.out.versions).match("versions_single_end_premade_index") } + ) + } + +'modules/nf-core/sortmerna/tests/tags.yml' is unchanged +'modules/nf-core/sortmerna/tests/premade_index.config' is unchanged +'modules/nf-core/sortmerna/tests/indexing_only.config' is unchanged +************************************************************ diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test index 4388cda0c..4103cc433 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test +++ b/modules/nf-core/sortmerna/tests/main.nf.test @@ -3,6 +3,9 @@ nextflow_process { name "Test Process SORTMERNA" script "../main.nf" process "SORTMERNA" + tag "modules" + tag "modules_nfcore" + tag "sortmerna" test("sarscov2 indexing only") { @@ -24,8 +27,10 @@ nextflow_process { assertAll( { assert process.success }, { assert ! process.out.reads }, - { assert snapshot(process.out.index).match("index_index_only") }, - { assert snapshot(process.out.versions).match("versions_index_only") } + { assert snapshot( + file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }, + process.out.versions + ).match() }, ) } @@ -89,7 +94,7 @@ nextflow_process { ).sort() ).match("sarscov2 single_end_match") }, - { assert snapshot(process.out.index).match("index_single_end") }, + { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_single_end") }, { assert snapshot(process.out.versions).match("versions_single_end") } ) } @@ -167,7 +172,7 @@ nextflow_process { ).sort() ).match("sarscov2 paired_end_match") }, - { assert snapshot(process.out.index).match("index_paired_end") }, + { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_paired_end") }, { assert snapshot(process.out.versions).match("versions_paired_end") } ) } @@ -262,7 +267,7 @@ nextflow_process { ).sort() ).match("sarscov2 single_end_premade_index_match") }, - { assert snapshot(process.out.index).match("index_single_end_premade_index") }, + { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }).match("index_single_end_premade_index") }, { assert snapshot(process.out.versions).match("versions_single_end_premade_index") } ) } diff --git a/modules/nf-core/sortmerna/tests/main.nf.test.snap b/modules/nf-core/sortmerna/tests/main.nf.test.snap index 86e84733b..0da75049c 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test.snap +++ b/modules/nf-core/sortmerna/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions_paired_end_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:27:11.223149" + "timestamp": "2024-10-22T10:40:01.533875274" }, "index_paired_end_stub": { "content": [ @@ -25,34 +25,41 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:24:25.384097178" + "timestamp": "2024-10-22T10:40:01.450465678" }, "versions_paired_end": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:27:04.517155" + "timestamp": "2024-10-22T10:39:48.811712136" }, - "versions_single_end_stub": { + "index_only_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + [ + { + "id": "test2" + }, + [ + + ] + ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-01T12:10:35.228450189" + "timestamp": "2024-10-22T10:38:56.554562414" }, "sarscov2 single_end_match": { "content": [ @@ -63,63 +70,65 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:23.20327" + "timestamp": "2024-10-22T10:39:09.015863183" }, - "index_only_stub": { + "versions_single_end_stub": { "content": [ [ - [ - { - "id": "test2" - }, - [ - - ] - ] + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:00:47.128504164" + "timestamp": "2024-10-22T10:39:28.573618474" }, "index_single_end_premade_index": { "content": [ [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:01:53.832643452" + "timestamp": "2024-10-22T10:40:14.159307146" }, "versions_single_end_premade_index": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-22T10:40:14.269803641" + }, + "sarscov2 indexing only": { + "content": [ + [ + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" + ], + [ + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:01:53.902154982" + "timestamp": "2024-10-22T10:38:39.794977786" }, "sarscov2 paired_end-for_stub_match": { "content": [ @@ -133,32 +142,24 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:56.063579" + "timestamp": "2024-10-22T10:40:01.365507281" }, "index_paired_end": { "content": [ [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:24:14.272659781" + "timestamp": "2024-10-22T10:39:48.72523749" }, "sarscov2 single_end_premade_index_match_stub": { "content": [ @@ -169,10 +170,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:05:01.913287272" + "timestamp": "2024-10-22T10:40:28.87594616" }, "sarscov2 single_end-for_stub_match": { "content": [ @@ -183,10 +184,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:29.197913" + "timestamp": "2024-10-22T10:39:28.458349619" }, "sarscov2 paired_end_match": { "content": [ @@ -200,46 +201,46 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-07T12:28:49.914992" + "timestamp": "2024-10-22T10:39:48.667990373" }, "versions_single_end": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:36:27.14244294" + "timestamp": "2024-10-22T10:39:09.110655329" }, - "versions_index_only": { + "versions_single_end_premade_index_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:00:35.609161481" + "timestamp": "2024-10-22T10:40:29.097777821" }, - "versions_single_end_premade_index_stub": { + "versions_index_only_stub": { "content": [ [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:05:02.059858431" + "timestamp": "2024-10-22T10:38:56.592840673" }, "index_single_end_stub": { "content": [ @@ -255,22 +256,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T14:23:58.068772508" - }, - "versions_index_only_stub": { - "content": [ - [ - "versions.yml:md5,7df9d50209f351e1f75e05a1fad6ba4b" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-26T15:00:47.169402699" + "timestamp": "2024-10-22T10:39:28.516407836" }, "index_single_end_premade_index_stub": { "content": [ @@ -286,54 +275,24 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:05:01.953316205" + "timestamp": "2024-10-22T10:40:28.988436085" }, "index_single_end": { "content": [ [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-26T14:36:26.88061978" - }, - "index_index_only": { - "content": [ - [ - [ - { - "id": "test2" - }, - [ - "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.stats:md5,67c9d4c768f28a450fc82a2b5d43db5c" - ] - ] + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:00:35.34089252" + "timestamp": "2024-10-22T10:39:09.050777261" }, "sarscov2 single_end_premade_index_match": { "content": [ @@ -344,9 +303,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-26T15:01:53.797737296" + "timestamp": "2024-10-22T10:40:14.075100849" } } \ No newline at end of file From d1ff982ce7e232e7e0023cd0a720d57ddcdf0e20 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 11:39:00 +0000 Subject: [PATCH 41/82] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0eb8458bc..5cde9cf6e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release - [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds - [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build +- [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From 7b56c844fb58a6ae1aa3d2d194ba0f6e0bb934bc Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 12:04:50 +0000 Subject: [PATCH 42/82] fix sortmerna tests for order --- modules/nf-core/sortmerna/tests/main.nf.test | 24 +++++++++++++++---- .../nf-core/sortmerna/tests/main.nf.test.snap | 24 +++++++++---------- 2 files changed, 32 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/sortmerna/tests/main.nf.test b/modules/nf-core/sortmerna/tests/main.nf.test index 4103cc433..4e1ced131 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test +++ b/modules/nf-core/sortmerna/tests/main.nf.test @@ -24,11 +24,15 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert ! process.out.reads }, { assert snapshot( - file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }, + index_files, process.out.versions ).match() }, ) @@ -81,6 +85,10 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert process.out.reads }, @@ -94,7 +102,7 @@ nextflow_process { ).sort() ).match("sarscov2 single_end_match") }, - { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_single_end") }, + { assert snapshot(index_files).match("index_single_end") }, { assert snapshot(process.out.versions).match("versions_single_end") } ) } @@ -159,6 +167,10 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert process.out.reads }, @@ -172,7 +184,7 @@ nextflow_process { ).sort() ).match("sarscov2 paired_end_match") }, - { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_paired_end") }, + { assert snapshot(index_files).match("index_paired_end") }, { assert snapshot(process.out.versions).match("versions_paired_end") } ) } @@ -254,6 +266,10 @@ nextflow_process { } then { + def index_files = file(process.out.index[0][1]).listFiles() + .findAll { !it.name.endsWith('.stats') } + .sort { a, b -> a.name <=> b.name } + assertAll( { assert process.success }, { assert process.out.reads }, @@ -267,7 +283,7 @@ nextflow_process { ).sort() ).match("sarscov2 single_end_premade_index_match") }, - { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }).match("index_single_end_premade_index") }, + { assert snapshot(index_files).match("index_single_end_premade_index") }, { assert snapshot(process.out.versions).match("versions_single_end_premade_index") } ) } diff --git a/modules/nf-core/sortmerna/tests/main.nf.test.snap b/modules/nf-core/sortmerna/tests/main.nf.test.snap index 0da75049c..07c2e3294 100644 --- a/modules/nf-core/sortmerna/tests/main.nf.test.snap +++ b/modules/nf-core/sortmerna/tests/main.nf.test.snap @@ -91,15 +91,15 @@ "content": [ [ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T10:40:14.159307146" + "timestamp": "2024-10-22T12:02:37.578808801" }, "versions_single_end_premade_index": { "content": [ @@ -117,8 +117,8 @@ "content": [ [ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ], [ "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" @@ -128,7 +128,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T10:38:39.794977786" + "timestamp": "2024-10-22T11:59:11.705138075" }, "sarscov2 paired_end-for_stub_match": { "content": [ @@ -151,15 +151,15 @@ "content": [ [ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T10:39:48.72523749" + "timestamp": "2024-10-22T12:01:29.664107565" }, "sarscov2 single_end_premade_index_match_stub": { "content": [ @@ -284,15 +284,15 @@ "content": [ [ "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", - "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", - "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" + "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", + "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T10:39:09.050777261" + "timestamp": "2024-10-22T12:00:30.580004574" }, "sarscov2 single_end_premade_index_match": { "content": [ From 82dfdf2580ab2ed99b6cad6cea4f87b9ac162e00 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 12:27:47 +0000 Subject: [PATCH 43/82] update a relevant pipeline test --- tests/remove_ribo_rna.nf.test.snap | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 8dedc7693..789571cfb 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -102,10 +102,10 @@ "bioconductor-summarizedexperiment": "1.32.0" }, "SORTMERNA": { - "sortmerna": "4.3.6" + "sortmerna": "4.3.7" }, "SORTMERNA_INDEX": { - "sortmerna": "4.3.6" + "sortmerna": "4.3.7" }, "STAR_ALIGN": { "star": "2.7.11b", @@ -1386,7 +1386,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T20:02:26.804814864" + "timestamp": "2024-10-22T12:24:58.795267716" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1420,7 +1420,7 @@ "gunzip": 1.1 }, "SORTMERNA_INDEX": { - "sortmerna": "4.3.6" + "sortmerna": "4.3.7" }, "STAR_GENOMEGENERATE": { "star": "2.7.11b", @@ -1482,6 +1482,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T20:03:16.221160765" + "timestamp": "2024-10-22T12:26:10.797017969" } } \ No newline at end of file From 0be2d6a53fb70c2f8afc7ce55debdea68eb30b6e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 14:02:56 +0100 Subject: [PATCH 44/82] Cut out module redundant software overrides --- conf/arm.config | 95 ------------------------------------------------- 1 file changed, 95 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 4a56788fe..cfcd283fa 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,92 +1,5 @@ process { - // - // Apply software overrides for ARM compatibility - // - - //// Tested, working, module updates in progress on main dev branch - - withName: 'CUSTOM_GETCHROMSIZES' { - conda = 'bioconda::samtools=1.21' - //conda = 'bioconda::samtools=1.20 bioconda::htslib=1.20' - } - - withName: 'CUSTOM_TX2GENE' { - conda = 'python=3.13.0' - //conda = 'python=3.9.5' - } - - withName: 'SALMON_INDEX|SALMON_QUANT' { - conda = 'bioconda::salmon=1.10.3' - //conda = 'bioconda::salmon=1.10.1' - } - - withName: 'SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS|SAMTOOLS_INDEX|SAMTOOLS_SORT|SAMTOOLS_STATS' { - conda = 'bioconda::samtools=1.21 bioconda::htslib' - //conda = 'bioconda::samtools=1.20 bioconda::htslib' - } - - withName: 'TRIMGALORE' { - conda = 'bioconda::trim-galore=0.6.10 bioconda::cutadapt=4.9' - //conda = 'bioconda::trim-galore=0.6.7 bioconda::cutadapt=3.4' - } - - withName: 'STRINGTIE_STRINGTIE' { - conda = 'bioconda::stringtie=2.2.3' - //conda = 'bioconda::stringtie=2.2.1' - } - - withName: 'SUBREAD_FEATURECOUNTS' { - conda = 'bioconda::subread=2.0.6' - //conda = 'bioconda::subread=2.0.1' - } - - withName: 'UCSC_BEDGRAPHTOBIGWIG' { - conda = 'bioconda::ucsc-bedgraphtobigwig=469' - //conda = 'bioconda::ucsc-bedgraphtobigwig=445' - } - - withName: 'BBSPLIT' { - conda = 'bioconda::bbmap=39.10' - // conda = 'bioconda::bbmap=39.01' - } - - withName: 'FQ_SUBSAMPLE' { - conda = 'bioconda::fq=0.12.0' - //conda = 'bioconda::fq=0.9.1' - } - - withName: 'KALLISTO_INDEX|KALLISTO_QUANT' { - conda = 'bioconda::kallisto=0.51.1' - //conda = 'bioconda::kallisto=0.48.0' - } - - withName: 'PRESEQ_LCEXTRAP' { - conda = 'bioconda::preseq=3.2.0' - //conda = 'bioconda::preseq=3.1.2' - } - - withName: 'CAT_ADDITIONAL_FASTA' { - conda = 'python=3.13.0' - //conda = 'conda-forge::coreutils=3.9.5' - } - - //// Proposed to nf-core with Seqera container - - // Seqera container, since coreutils in existing image (ubuntu) wouldn't - // match update - withName: 'CAT_FASTQ' { - conda = 'conda-forge::coreutils=9.5' - //conda = 'conda-forge::coreutils=8.30' - } - - // Seqera container to avoid updating a mulled container - - withName: 'STAR_ALIGN|STAR_GENOMEGENERATE' { - conda = 'bioconda::star2.7.11b bioconda::samtools=1.21 bioconda::htslib=1.21 conda-forge::gawk=5.1.0' - //conda = 'bioconda::star=2.7.10a bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::gawk=5.1.0' - } - //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds @@ -123,12 +36,4 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} - //// c) have aarch64 builds in bioconda, but with problems - // sortmerna gives 'illegal instruction' errors at 5.3.7 with either - // Biocontainers or Seqera Containers - withName: 'SORTMERNA' { - conda = 'bioconda::sortmerna=4.3.7' - //conda = 'bioconda::sortmerna=4.3.6' - } - } From ed026be0c3bd823b1f01060c06180e8db39c0d24 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 17:42:03 +0100 Subject: [PATCH 45/82] Add frozen ARM builds --- conf/arm.config | 212 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 211 insertions(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index cfcd283fa..c8d3c379f 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,9 +1,219 @@ process { + //// Frozen ARM buids from Wave + + withName: GTF_FILTER { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } + } + + withName: PREPROCESS_TRANSCRIPTS_FASTA_GENCODE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } + } + + withName: DESEQ2_QC { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } + } + + withName: GTF2BED { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } + } + + withName: MULTIQC_CUSTOM_BIOTYPE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } + } + + withName: RSEM_MERGE_COUNTS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } + } + + withName: UCSC_BEDCLIP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } + } + + withName: UCSC_BEDGRAPHTOBIGWIG { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } + } + + withName: CAT_FASTQ { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } + } + + withName: RSEQC_TIN { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_READDISTRIBUTION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_JUNCTIONSATURATION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_READDUPLICATION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_INFEREXPERIMENT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_BAMSTAT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_INNERDISTANCE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: RSEQC_JUNCTIONANNOTATION { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } + } + + withName: PICARD_MARKDUPLICATES { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } + } + + withName: QUALIMAP_RNASEQ { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } + } + + withName: SUBREAD_FEATURECOUNTS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } + } + + withName: MULTIQC { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' } + } + + withName: STRINGTIE_STRINGTIE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } + } + + withName: UNTAR { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } + } + + withName: FQ_SUBSAMPLE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } + } + + withName: DUPRADAR { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } + } + + withName: SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } + } + + withName: STAR_GENOMEGENERATE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + } + + withName: STAR_ALIGN { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } + } + + withName: TXIMETA_TXIMPORT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } + } + + withName: SORTMERNA { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } + } + + withName: PRESEQ_LCEXTRAP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } + } + + withName: BEDTOOLS_GENOMECOV { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } + } + + withName: BBMAP_BBSPLIT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } + } + + withName: FASTQC { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } + } + + withName: KALLISTO_QUANT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } + } + + withName: KALLISTO_INDEX { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } + } + + withName: SAMTOOLS_SORT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_IDXSTATS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_INDEX { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_FLAGSTAT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: SAMTOOLS_STATS { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: CUSTOM_CATADDITIONALFASTA { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } + } + + withName: CUSTOM_TX2GENE { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } + } + + withName: CUSTOM_GETCHROMSIZES { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } + } + + withName: UMITOOLS_PREPAREFORRSEM { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: UMITOOLS_EXTRACT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: UMITOOLS_DEDUP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } + } + + withName: GFFREAD { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } + } + + withName: FASTP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } + } + + withName: SALMON_QUANT { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } + } + + withName: SALMON_INDEX { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } + } + + withName: GUNZIP { + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } + } + //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds - + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' From a8d514f79220ffd10a0cb6b7e0d6acd5714ef179 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 18:16:26 +0100 Subject: [PATCH 46/82] Container directives for conda overrides --- conf/arm.config | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index c8d3c379f..b80fe295c 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -215,23 +215,31 @@ process { //// a) have seqera aarch64 conda builds withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' + + conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'RSEM_PREPAREREFERENCE' { - conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + + conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } withName: 'RSEM_CALCULATEEXPRESSION' { - conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' + + conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } //// b) need aarch64 conda builds From 8e147116f934f6e31788307bd5a472d8032521f6 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 18:38:07 +0100 Subject: [PATCH 47/82] Temporary Trimgalore override, singularity fixes for rsem processes --- conf/arm.config | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index b80fe295c..ef488cc05 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -210,6 +210,18 @@ process { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } + //// Remove this once we've got a new Biocontainer for trimgalore with the + //// newer cutadapt, and we've update the nf-core module + //// https://github.com/bioconda/bioconda-recipes/pull/51563 + + withName: TRIMGALORE { + //conda = 'bioconda::cutadapt=4.2 trim-galore=0.6.10' + + conda = 'bioconda::cutadapt=4.9 trim-galore=0.6.10' + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0dda1e09d10d1e2994ea85843b1e3d62212598ca5047e0ab419d5d87db637057/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:1cd58fa242e634da' } + + } + //// No aarch64 builds in bioconda / conda-forge channels //// a) have seqera aarch64 conda builds @@ -232,14 +244,14 @@ process { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } withName: 'RSEM_CALCULATEEXPRESSION' { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } //// b) need aarch64 conda builds From 161cf95412b8a7ae40ba34d499ae783c94e47b6d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 18:49:37 +0100 Subject: [PATCH 48/82] update docs --- docs/usage.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index ad2aa4e26..c9302fa1f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -116,6 +116,10 @@ If you would like to reduce the number of reads used in the analysis, for exampl ## Alignment options +:::note +Not currently available using ARM architecture ('-profile arm') +::: + By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. You also have the option to pseudoalign and quantify your data directly with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by specifying `salmon` or `kallisto` to the `--pseudo_aligner` parameter. The selected pseudoaligner will then be run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon or Kallisto in isolation. By default, the pipeline will use the genome fasta and gtf file to generate the transcripts fasta file, and then to build the Salmon index. You can override these parameters using the `--transcript_fasta` and `--salmon_index` parameters, respectively. @@ -298,6 +302,10 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options +:::note +Not currently available using ARM architecture ('-profile arm') +::: + The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. It is important to note that the accuracy of Kraken2 is [highly dependent on the database](https://doi.org/10.1099/mgen.0.000949) used. Specifically, it is [crucial](https://doi.org/10.1128/mbio.01607-23) to ensure that the host genome is included in the database. If you are particularly concerned about certain contaminants, it may be beneficial to use a smaller, more focused database containing primarily those contaminants instead of the full standard database. Various pre-built databases [are available for download](https://benlangmead.github.io/aws-indexes/k2), and instructions for building a custom database can be found in the [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown). Additionally, genomes of contaminants detected in previous sequencing experiments are available on the [OpenContami website](https://openlooper.hgc.jp/opencontami/help/help_oct.php). @@ -420,6 +428,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. + - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. ### `-resume` From caad7fa623a0e88ad2a07cfd80493adc1032bd76 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 20:07:50 +0100 Subject: [PATCH 49/82] Fix argument conflict between STAR versions --- subworkflows/local/align_star/nextflow.config | 68 +++++++++++-------- 1 file changed, 40 insertions(+), 28 deletions(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 3d07c9e88..b676150dd 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -1,36 +1,48 @@ +def generateStarAlignArgs(save_unaligned, contaminant_screening, extra_star_align_args) { + def argsToMap = { String args -> + args.split(/\s(?=--)/).collectEntries { + def parts = it.trim().split(/\s+/, 2) + [(parts[0]): parts.size() > 1 ? parts[1] : ''] + } + } + + def base_args = """ + --quantMode TranscriptomeSAM + --twopassMode Basic + --outSAMtype BAM Unsorted + --readFilesCommand zcat + --runRNGseed 0 + --outFilterMultimapNmax 20 + --alignSJDBoverhangMin 1 + --outSAMattributes NH HI AS NM MD + --outSAMstrandField intronMotif + """.trim() + + if (save_unaligned || contaminant_screening) { + base_args += "\n--outReadsUnmapped Fastx" + } + + def final_args_map = argsToMap(base_args) + (extra_star_align_args ? argsToMap(extra_star_align_args) : [:]) + final_args_map.collect { key, value -> "${key} ${value}".trim() }.join(' ') +} + if (!params.skip_alignment && params.aligner == 'star_salmon') { process { - withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - ext.args = { - // Function to convert argument strings into a map - def argsToMap = { String args -> - args.split("\\s(?=--)").collectEntries { - def parts = it.trim().split(/\s+/, 2) - [(parts.first()): parts.last()] - } - } - - // Initialize the map with preconfigured values - def preset_args_map = argsToMap(""" - --quantMode TranscriptomeSAM - --twopassMode Basic - --outSAMtype BAM Unsorted - --readFilesCommand zcat - --runRNGseed 0 - --outFilterMultimapNmax 20 - --alignSJDBoverhangMin 1 - --outSAMattributes NH HI AS NM MD - --quantTranscriptomeSAMoutput BanSingleEnd - --outSAMstrandField intronMotif - ${params.save_unaligned || params.contaminant_screening ? '--outReadsUnmapped Fastx' : ''} - """.trim()) - // Consolidate the extra arguments - def final_args_map = preset_args_map + (params.extra_star_align_args ? argsToMap(params.extra_star_align_args) : [:]) + // We have to condition this, because the args are slightly different between the latest STAR and the one compatible with iGenomes - // Convert the map back to a list and then to a single string - final_args_map.collect { key, value -> "${key} ${value}" }.join(' ').trim() + withName: '.*:ALIGN_STAR:STAR_ALIGN' { + ext.args = { + generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') + } + } + withName: 'ALIGN_STAR:STAR_ALIGN_IGENOMES' { + ext.args = { + generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend') } + + } + withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { publishDir = [ [ From cdfb98b9dcb1512392c05af947bab2a637e21d12 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 19:50:23 +0000 Subject: [PATCH 50/82] Fix config error --- subworkflows/local/align_star/nextflow.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index b676150dd..86960b2e1 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -36,11 +36,10 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') } } - withName: 'ALIGN_STAR:STAR_ALIGN_IGENOMES' { + withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { ext.args = { generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend') } - } withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { From 524e19eacb6b80a72bb8460f3e4e6f5f096f2254 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 21:44:55 +0100 Subject: [PATCH 51/82] Correction to star rsem --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index ef488cc05..3a2b63d9b 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -250,7 +250,7 @@ process { withName: 'RSEM_CALCULATEEXPRESSION' { //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d' + conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } From 4f8de9450eaa6ac691afb1cad146b271f3a5e760 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 22:17:41 +0100 Subject: [PATCH 52/82] Refine config setup --- subworkflows/local/align_star/nextflow.config | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config index 86960b2e1..106710e05 100644 --- a/subworkflows/local/align_star/nextflow.config +++ b/subworkflows/local/align_star/nextflow.config @@ -33,12 +33,20 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') { withName: '.*:ALIGN_STAR:STAR_ALIGN' { ext.args = { - generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeSAMoutput BanSingleEnd') + generateStarAlignArgs( + params.save_unaligned, + params.contaminant_screening, + (params.extra_star_align_args ?: '') + ' --quantTranscriptomeSAMoutput BanSingleEnd' + ) } } withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { ext.args = { - generateStarAlignArgs(params.save_unaligned, params.contaminant_screening, params.extra_star_align_args + ' --quantTranscriptomeBan Singleend') + generateStarAlignArgs( + params.save_unaligned, + params.contaminant_screening, + (params.extra_star_align_args ?: '') + ' --quantTranscriptomeBan Singleend' + ) } } withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { From a1d558e57e051453dfcd409fee20a4431d43b4f4 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 22:30:32 +0100 Subject: [PATCH 53/82] Bump trimgalore module --- modules.json | 4 +- modules/nf-core/trimgalore/environment.yml | 2 +- modules/nf-core/trimgalore/main.nf | 4 +- .../trimgalore/tests/main.nf.test.snap | 20 ++++---- .../tests/main.nf.test | 10 ++++ .../tests/main.nf.test.snap | 48 +++++++++---------- 6 files changed, 49 insertions(+), 39 deletions(-) diff --git a/modules.json b/modules.json index 7f889aeec..61692d607 100644 --- a/modules.json +++ b/modules.json @@ -245,7 +245,7 @@ }, "trimgalore": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { @@ -333,7 +333,7 @@ }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 910ffa882..622407eda 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=4.2 + - bioconda::cutadapt=4.9 - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 30d17edc1..8a2fc54b3 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 61b3504a9..21da84933 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:50:36.440264431" + "timestamp": "2024-10-22T19:23:17.969056957" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -80,7 +80,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:50:51.25902234" + "timestamp": "2024-10-22T19:23:28.617831159" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ], "zip": [ @@ -163,18 +163,18 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:51:19.024228479" + "timestamp": "2024-10-22T19:23:51.539787731" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:51:02.471703095" + "timestamp": "2024-10-22T19:23:41.16485915" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 1043d06ad..96e05765b 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -5,6 +5,16 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_fastqc_umitools_trimgalore" + tag "fastqc" + tag "umitools/extract" + tag "trimgalore" + + tag "FASTQC" + tag "UMITOOLS_EXTRACT" + tag "TRIMGALORE" test("test single end read with UMI") { diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index f8a746aa6..834aaa931 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -61,8 +61,8 @@ ], "9": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -123,8 +123,8 @@ ], "versions": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], @@ -132,7 +132,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:56.222595833" + "timestamp": "2024-10-22T19:25:19.153139356" }, "test paired end read without UMI - stub": { "content": [ @@ -192,8 +192,8 @@ ] ], "9": [ - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -250,8 +250,8 @@ ], "versions": [ - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], @@ -259,7 +259,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:19:07.775855857" + "timestamp": "2024-10-22T19:25:30.433084765" }, "test paired end read without UMI": { "content": [ @@ -288,15 +288,15 @@ ], [ - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:19.621101515" + "timestamp": "2024-10-22T19:24:40.341840093" }, "test single end read with UMI": { "content": [ @@ -323,15 +323,15 @@ ], [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:17:51.049984482" + "timestamp": "2024-10-22T19:24:09.307037853" }, "test paired end read with UMI": { "content": [ @@ -358,15 +358,15 @@ ], [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:07.106739839" + "timestamp": "2024-10-22T19:24:26.93011239" }, "test skip all steps": { "content": [ @@ -448,8 +448,8 @@ ], "9": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ], "fastqc_html": [ [ @@ -510,8 +510,8 @@ ], "versions": [ "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", - "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", - "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" + "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2", + "versions.yml:md5,c1bbaea7bd77a49018d36e859e297118" ] } ], @@ -519,6 +519,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-18T12:18:42.513733457" + "timestamp": "2024-10-22T19:25:05.585472049" } } \ No newline at end of file From dae2899782f635e89450a3c2ad87d5348224b5c3 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 22 Oct 2024 22:38:34 +0100 Subject: [PATCH 54/82] Fix up ARM profile for updated trim-galore --- conf/arm.config | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 3a2b63d9b..322a239e7 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -210,15 +210,8 @@ process { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } - //// Remove this once we've got a new Biocontainer for trimgalore with the - //// newer cutadapt, and we've update the nf-core module - //// https://github.com/bioconda/bioconda-recipes/pull/51563 - withName: TRIMGALORE { - //conda = 'bioconda::cutadapt=4.2 trim-galore=0.6.10' - - conda = 'bioconda::cutadapt=4.9 trim-galore=0.6.10' - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0dda1e09d10d1e2994ea85843b1e3d62212598ca5047e0ab419d5d87db637057/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:1cd58fa242e634da' } + container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' } } From d3580a4bc96d74b623dfecddff73ad4c08b7e7ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:38:26 +0100 Subject: [PATCH 55/82] Apply suggestions from code review Co-authored-by: Harshil Patel --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index c9302fa1f..1e3261e90 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -117,7 +117,7 @@ If you would like to reduce the number of reads used in the analysis, for exampl ## Alignment options :::note -Not currently available using ARM architecture ('-profile arm') +The `--aligner hisat2` option is not currently supported using ARM architecture ('-profile arm') ::: By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `--aligner star_salmon`) to map the raw FastQ reads to the reference genome, project the alignments onto the transcriptome and to perform the downstream BAM-level quantification with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html). STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. Since the [RSEM](https://github.com/deweylab/RSEM) (i.e. `--aligner star_rsem`) workflow in the pipeline also uses STAR you should use the [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) aligner (i.e. `--aligner hisat2`) if you have memory limitations. From 32f7d3245b2a73f3ca0b87387723070f08017e90 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:42:54 +0100 Subject: [PATCH 56/82] Apply suggestions from code review Co-authored-by: Harshil Patel --- conf/arm.config | 15 +++++++++------ modules/nf-core/trimgalore/main.nf | 2 +- .../tests/main.nf.test | 10 ---------- 3 files changed, 10 insertions(+), 17 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index 322a239e7..ad4fb2eb9 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,6 +1,8 @@ process { - //// Frozen ARM buids from Wave + // + // Tools that have native Conda builds for AMD and ARM + // withName: GTF_FILTER { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } @@ -215,13 +217,12 @@ process { } - //// No aarch64 builds in bioconda / conda-forge channels + // + // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in seqera Conda channel. + // - //// a) have seqera aarch64 conda builds withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { - //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } @@ -247,7 +248,9 @@ process { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } - //// b) need aarch64 conda builds + // + // Tools currently unsupported for ARM + // //withName: 'HISAT2_ALIGN' { // conda = 'bioconda::hisat2 bioconda::samtools' diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 8a2fc54b3..02f4b16ad 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,7 +4,7 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_1' : 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test index 96e05765b..1043d06ad 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test @@ -5,16 +5,6 @@ nextflow_workflow { workflow "FASTQ_FASTQC_UMITOOLS_TRIMGALORE" config './nextflow.config' - tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/fastq_fastqc_umitools_trimgalore" - tag "fastqc" - tag "umitools/extract" - tag "trimgalore" - - tag "FASTQC" - tag "UMITOOLS_EXTRACT" - tag "TRIMGALORE" test("test single end read with UMI") { From 7df162fcb3f50f4a1e3d91025cb45a9784214f1b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:47:57 +0100 Subject: [PATCH 57/82] Add notes for kraken2/ braken --- conf/arm.config | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index ad4fb2eb9..b01e09465 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -262,4 +262,10 @@ process { // //conda = 'bioconda::hisat2=2.2.1' //} -} + // withName: 'KRAKEN2_KRAKEN2' { + // conda = 'bioconda::kraken2=2.1.3 coreutils=9.4 pigz=2.8' + //} + + // withName: 'BRACKEN_BRACKEN' { + // conda = 'bioconda::bracken=2.9' + //} From 642d2a869d76322711941850fd54a53c2097f43a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:07:55 +0100 Subject: [PATCH 58/82] Update docs --- docs/usage.md | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 1e3261e90..26be822fd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -303,7 +303,7 @@ By default, the input GTF file will be filtered to ensure that sequence names co ## Contamination screening options :::note -Not currently available using ARM architecture ('-profile arm') +The `--contaminant_screening` option is not currently available using ARM architecture ('-profile arm') ::: The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2. @@ -364,6 +364,26 @@ genome: 'GRCh37' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). +### Running on Linux ARM architectures + +The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: + +```bash +nextflow run \ + nf-core/rnaseq \ + --input \ + --outdir \ + --gtf \ + --fasta \ + -profile docker,arm +``` + +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. + +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -428,8 +448,13 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. +- `arm` - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + ### `-resume` Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). From d9e534da8860a5b07c3f3577fcc5248f74d60f41 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:08:52 +0100 Subject: [PATCH 59/82] prettier --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 26be822fd..581ed9598 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -366,7 +366,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c ### Running on Linux ARM architectures -The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: +The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: ```bash nextflow run \ @@ -378,7 +378,7 @@ nextflow run \ -profile docker,arm ``` -This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. :::warning Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. From d4fcb5602f06e41ed204d5536c143dfc2ba0a8f5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:11:31 +0100 Subject: [PATCH 60/82] lint fix --- conf/arm.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/arm.config b/conf/arm.config index b01e09465..c28d97099 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -265,7 +265,7 @@ process { // withName: 'KRAKEN2_KRAKEN2' { // conda = 'bioconda::kraken2=2.1.3 coreutils=9.4 pigz=2.8' //} - + // withName: 'BRACKEN_BRACKEN' { // conda = 'bioconda::bracken=2.9' //} From 896dd74cf8a669714ee829f5ff355f32a6f52ecd Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 10:36:47 +0000 Subject: [PATCH 61/82] [skip ci] Reorg ARM bits --- docs/usage.md | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 581ed9598..851e20c7d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -366,6 +366,10 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c ### Running on Linux ARM architectures +:::warning +Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. +::: + The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example: ```bash @@ -378,11 +382,7 @@ nextflow run \ -profile docker,arm ``` -This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. - -:::warning -Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. -::: +This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operations. ### Updating the pipeline @@ -449,11 +449,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. - `arm` - - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. - -:::warning -Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability. -::: + - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments. See [Running on Linux ARM architectures](#running-on-linux-arm-architectures). ### `-resume` From 314ea855fcc6bb55546adffb9f880280c917a68e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 23 Oct 2024 12:37:19 +0200 Subject: [PATCH 62/82] Update arm.config --- conf/arm.config | 134 ++++++++++++++++++++++++------------------------ 1 file changed, 68 insertions(+), 66 deletions(-) diff --git a/conf/arm.config b/conf/arm.config index c28d97099..5169bbc6a 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -1,249 +1,253 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running the pipeline with ARM architecture +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines custom containers and Conda definitions required to run pipeline with ARM. + + Use as follows: + nextflow run nf-core/rnaseq -profile ,arm + +---------------------------------------------------------------------------------------- +*/ + process { // // Tools that have native Conda builds for AMD and ARM // - withName: GTF_FILTER { + withName: 'GTF_FILTER' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } - withName: PREPROCESS_TRANSCRIPTS_FASTA_GENCODE { + withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } - withName: DESEQ2_QC { + withName: 'DESEQ2_QC' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/70/70a3d17733d2c21cff464c31a7a57438cea528bea84c675b7c474eaa7f075f57/data' : 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } } - withName: GTF2BED { + withName: 'GTF2BED' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } } - withName: MULTIQC_CUSTOM_BIOTYPE { + withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } } - withName: RSEM_MERGE_COUNTS { + withName: 'RSEM_MERGE_COUNTS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4ad78019c37ff4ab22c0dff6ab1af655c6438562ef644d0323861a97971d7694/data' : 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } } - withName: UCSC_BEDCLIP { + withName: 'UCSC_BEDCLIP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5f/5f559cabdfda8b2937c4213d3a53547eb882b2fc8cc36ebfeff07481fa47823a/data' : 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } } - withName: UCSC_BEDGRAPHTOBIGWIG { + withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/389312a4a6022c5f5d2510dfa9bedb0491b36c8a27e8d842c05de00bc3b5be76/data' : 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } } - withName: CAT_FASTQ { + withName: 'CAT_FASTQ' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/38/38d3638640600b355110f9bca56c514e3cc068bf96b8b68f98cba2a59a053505/data' : 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } } - withName: RSEQC_TIN { + withName: 'RSEQC_TIN' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_READDISTRIBUTION { + withName: 'RSEQC_READDISTRIBUTION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_JUNCTIONSATURATION { + withName: 'RSEQC_JUNCTIONSATURATION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_READDUPLICATION { + withName: 'RSEQC_READDUPLICATION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_INFEREXPERIMENT { + withName: 'RSEQC_INFEREXPERIMENT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_BAMSTAT { + withName: 'RSEQC_BAMSTAT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_INNERDISTANCE { + withName: 'RSEQC_INNERDISTANCE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: RSEQC_JUNCTIONANNOTATION { + withName: 'RSEQC_JUNCTIONANNOTATION' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6306dc454d7a565c726e30b9da0b9070fc67555516a660c54e7baba365070b25/data' : 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } } - withName: PICARD_MARKDUPLICATES { + withName: 'PICARD_MARKDUPLICATES' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c0/c0d4bbb10417a70d137a28da09329d9f9fbdf964a1cfeda24b05b618cae6b16f/data' : 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } } - withName: QUALIMAP_RNASEQ { + withName: 'QUALIMAP_RNASEQ' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7a/7aa0998788d327c6e7104c2c1e7bea2e8bb8fb7076ec5de3fdab4027e501b9a9/data' : 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } } - withName: SUBREAD_FEATURECOUNTS { + withName: 'SUBREAD_FEATURECOUNTS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } } - withName: MULTIQC { + withName: 'MULTIQC' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6e97dcafc5915f90f863e70153f96bbe47963ebfd08383454d8bcd7263696e4e/data' : 'community.wave.seqera.io/library/multiqc:1.25.1--4062a515975cacba' } } - withName: STRINGTIE_STRINGTIE { + withName: 'STRINGTIE_STRINGTIE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } } - withName: UNTAR { + withName: 'UNTAR' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } - withName: FQ_SUBSAMPLE { + withName: 'FQ_SUBSAMPLE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b0/b00189d4f7eed55199354a3dff8a9a535e1dfb3a2f4c97f5d0bf9e388105795e/data' : 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } } - withName: DUPRADAR { + withName: 'DUPRADAR' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10141f8fd43964316d04214a5f7d99a62e11cdbab5bd2fcd4f7c3c06eca9f2f6/data' : 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } } - withName: SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT { + withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a7/a7d1ef576617b9790973bc9d178c4ef136a52b6337260c536cff6cd68f103b45/data' : 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } } - withName: STAR_GENOMEGENERATE { + withName: 'STAR_GENOMEGENERATE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } } - withName: STAR_ALIGN { + withName: 'STAR_ALIGN' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a2d5226e4ce3dee8b29154c16a87d282d96c76e75b6678d032643902591586e2/data' : 'community.wave.seqera.io/library/htslib_samtools_star_gawk:1d1b7da208684cac' } } - withName: TXIMETA_TXIMPORT { + withName: 'TXIMETA_TXIMPORT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f89ab1fef6e38e572ad1844d06f6d3d334d2b19a70c9e5d87bfc862b88728c23/data' : 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } } - withName: SORTMERNA { + withName: 'SORTMERNA' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f161ea3d4083b7d8fcbf8524cb5ab69f386b4e36b771bb5abf9ccf8ab29e9775/data' : 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } } - withName: PRESEQ_LCEXTRAP { + withName: 'PRESEQ_LCEXTRAP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5ab535d5b4c88dc4837cab00919d4d5ea66dd4d6dc837d841886bef72145f435/data' : 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } } - withName: BEDTOOLS_GENOMECOV { + withName: 'BEDTOOLS_GENOMECOV' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/51/519a920dacc643078823740486c40d30b9f555c493217d9f72db04901350e009/data' : 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } } - withName: BBMAP_BBSPLIT { + withName: 'BBMAP_BBSPLIT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/63ca91c8bf7285296777de219e5d5a71d2a7de47599cbc94441aced7868a4f83/data' : 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } } - withName: FASTQC { + withName: 'FASTQC' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fd/fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017/data' : 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } } - withName: KALLISTO_QUANT { + withName: 'KALLISTO_QUANT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } - withName: KALLISTO_INDEX { + withName: 'KALLISTO_INDEX' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/24/24655791b5db39ffdfffa8e5aeabfd11dda4553b5311ddb22e724c38b1591e8d/data' : 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } } - withName: SAMTOOLS_SORT { + withName: 'SAMTOOLS_SORT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_IDXSTATS { + withName: 'SAMTOOLS_IDXSTATS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_INDEX { + withName: 'SAMTOOLS_INDEX' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_FLAGSTAT { + withName: 'SAMTOOLS_FLAGSTAT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: SAMTOOLS_STATS { + withName: 'SAMTOOLS_STATS' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: CUSTOM_CATADDITIONALFASTA { + withName: 'CUSTOM_CATADDITIONALFASTA' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c1/c17acd739990ad12c06583f57b097014c2bde5a91d0977fd102864a82f95e136/data' : 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } } - withName: CUSTOM_TX2GENE { + withName: 'CUSTOM_TX2GENE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/60/6029f43341dc0bea31d14c2ce4c779d7a48dfed6ecb29ce1630b8378c560c490/data' : 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } } - withName: CUSTOM_GETCHROMSIZES { + withName: 'CUSTOM_GETCHROMSIZES' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b993d5094fcf4fe7e5016b9118363a8e9dc1a48e35964e5f15465ba4a65739e9/data' : 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } } - withName: UMITOOLS_PREPAREFORRSEM { + withName: 'UMITOOLS_PREPAREFORRSEM' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } - withName: UMITOOLS_EXTRACT { + withName: 'UMITOOLS_EXTRACT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } - withName: UMITOOLS_DEDUP { + withName: 'UMITOOLS_DEDUP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ba/ba7c02244236db73a56ff1eb880b16c2dd53679834e1b72bb096e1f633e35644/data' : 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } } - withName: GFFREAD { + withName: 'GFFREAD' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } } - withName: FASTP { + withName: 'FASTP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7e/7ec6234f24305b9694b89de0352fff942ce1d68f840184020b0b9135bc54bda1/data' : 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } } - withName: SALMON_QUANT { + withName: 'SALMON_QUANT' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } - withName: SALMON_INDEX { + withName: 'SALMON_INDEX' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b8/b8e3bcb1daa42497d0159cd5ae3b6d164b4470a972dd72d9d10b365fa166e5a4/data' : 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } } - withName: GUNZIP { + withName: 'GUNZIP' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4bcb36d5e1fb90c8af0171a83b792ada446b04feb4ac3f26d0ce550d3c678383/data' : 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } } - withName: TRIMGALORE { + withName: 'TRIMGALORE' { container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10e7b91ef06bdf5790120809afc8cf36aac0261b618d810c952d5afd60dd5ed2/data' : 'community.wave.seqera.io/library/cutadapt_trim-galore:2aa2fc797328573b' } - } // - // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in seqera Conda channel. + // Tools that do not have native Conda builds for AMD and ARM. Required custom builds in 'seqera' Conda channel. // - withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' { conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'STAR_GENOMEGENERATE_IGENOMES' { - //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0' - conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' } } withName: 'RSEM_PREPAREREFERENCE' { - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } withName: 'RSEM_CALCULATEEXPRESSION' { - //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a' - conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a' container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3/data' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' } } @@ -253,13 +257,11 @@ process { // //withName: 'HISAT2_ALIGN' { - // conda = 'bioconda::hisat2 bioconda::samtools' - // //conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' + // conda = 'bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1' //} //withName: 'HISAT2_BUILD|HISAT2_EXTRACTSPLICESITES' { - // conda = 'bioconda::hisat2' - // //conda = 'bioconda::hisat2=2.2.1' + // conda = 'bioconda::hisat2=2.2.1' //} // withName: 'KRAKEN2_KRAKEN2' { From 251481f075e573ad2dba0e75366fd620999cf9c1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 11:59:43 +0100 Subject: [PATCH 63/82] Fix syntax error --- conf/arm.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/arm.config b/conf/arm.config index c28d97099..8f84cdeb0 100644 --- a/conf/arm.config +++ b/conf/arm.config @@ -269,3 +269,4 @@ process { // withName: 'BRACKEN_BRACKEN' { // conda = 'bioconda::bracken=2.9' //} +} From f59132afa965188eed35d3504f6b6688b0d21599 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 12:28:10 +0000 Subject: [PATCH 64/82] revert trimgalore tweak to appease linter --- modules/nf-core/trimgalore/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 02f4b16ad..8a2fc54b3 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,7 +4,7 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_1' : + 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" input: From 40f05c5dcaa50b911116e804d6510f8e34443635 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 12:28:23 +0000 Subject: [PATCH 65/82] Update pipeline-level tests --- tests/default.nf.test.snap | 18 +++++++++--------- tests/featurecounts_group_type.nf.test.snap | 18 +++++++++--------- tests/hisat2.nf.test.snap | 18 +++++++++--------- tests/kallisto.nf.test.snap | 18 +++++++++--------- tests/min_mapped_reads.nf.test.snap | 18 +++++++++--------- tests/remove_ribo_rna.nf.test.snap | 18 +++++++++--------- tests/salmon.nf.test.snap | 18 +++++++++--------- tests/skip_qc.nf.test.snap | 18 +++++++++--------- tests/star_rsem.nf.test.snap | 18 +++++++++--------- 9 files changed, 81 insertions(+), 81 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d50bdafc0..b70ad3971 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -37,7 +37,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:47:30.454374101" + "timestamp": "2024-10-23T10:43:40.33664602" }, "Params: default": { "content": [ @@ -212,7 +212,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1300,18 +1300,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1459,6 +1459,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:14:46.845308285" + "timestamp": "2024-10-23T10:42:45.202573855" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index d72672710..bbe39ddd6 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -37,7 +37,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -90,7 +90,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T18:52:01.516368536" + "timestamp": "2024-10-23T10:54:29.62339584" }, "Params: --featurecounts_group_type false": { "content": [ @@ -206,7 +206,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1266,18 +1266,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1409,6 +1409,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:24:36.371474446" + "timestamp": "2024-10-23T10:53:28.969150716" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 62e0b952f..78d8c3ad4 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -35,7 +35,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_HISAT2_INDEX": { "untar": 1.34 @@ -91,7 +91,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:42:22.430556863" + "timestamp": "2024-10-23T11:01:31.33505759" }, "Params: --aligner hisat2": { "content": [ @@ -206,7 +206,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1247,18 +1247,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1309,6 +1309,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:41:24.698018172" + "timestamp": "2024-10-23T11:00:43.422573373" } } \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index e48e6895f..8aea96806 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -47,7 +47,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -236,24 +236,24 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233" + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:46:36.506804194" + "timestamp": "2024-10-23T11:04:57.579312846" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -288,7 +288,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -329,6 +329,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T15:47:47.272256089" + "timestamp": "2024-10-23T11:05:54.052864085" } } \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 2f4db1480..e11236066 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -119,7 +119,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1041,19 +1041,19 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1175,7 +1175,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:45:32.241828903" + "timestamp": "2024-10-23T11:18:04.553985917" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1215,7 +1215,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1268,6 +1268,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T19:46:21.485818867" + "timestamp": "2024-10-23T11:19:22.443482528" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 789571cfb..79b4954b9 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -125,7 +125,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1227,18 +1227,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba", "multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1386,7 +1386,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T12:24:58.795267716" + "timestamp": "2024-10-23T11:36:09.902195192" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1429,7 +1429,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -1482,6 +1482,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-22T12:26:10.797017969" + "timestamp": "2024-10-23T11:37:11.90905171" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index a83151bbb..aa517a395 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -41,7 +41,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -281,17 +281,17 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", @@ -329,7 +329,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:22:14.604923669" + "timestamp": "2024-10-23T11:41:47.859384178" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -361,7 +361,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -402,6 +402,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:23:12.380483903" + "timestamp": "2024-10-23T11:42:36.34114827" } } \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index cb94364bb..0589bb509 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -34,7 +34,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_SALMON_INDEX": { "untar": 1.34 @@ -76,7 +76,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T20:14:28.433411196" + "timestamp": "2024-10-23T11:50:42.323505833" }, "Params: --skip_qc": { "content": [ @@ -154,7 +154,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -681,17 +681,17 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -787,6 +787,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T20:13:44.078197492" + "timestamp": "2024-10-23T11:49:49.131172185" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index a68d337c2..c396c1a4a 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -116,7 +116,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "TXIMETA_TXIMPORT": { "bioconductor-tximeta": "1.20.1" @@ -1138,18 +1138,18 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878", "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", - "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", - "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db", "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", - "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa", + "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", + "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_featurecounts_biotype_plot.txt:md5,aef45c9c7814f3127cd3e9b77a5ed676", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1270,7 +1270,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:29:54.475156285" + "timestamp": "2024-10-23T12:16:02.205058346" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1305,7 +1305,7 @@ }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.2 + "cutadapt": 4.9 }, "UNTAR_RSEM_INDEX": { "untar": 1.34 @@ -1361,6 +1361,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-21T16:31:04.240180676" + "timestamp": "2024-10-23T12:17:33.292700445" } } \ No newline at end of file From 79370d35cac0f54f442e592ee52a36db61dfb96a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 13:54:14 +0100 Subject: [PATCH 66/82] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5cde9cf6e..cacba7c82 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds - [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build - [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility +- [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From 9b9181c2f0bc6233ea5991628d7c469dc027f11d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 14:31:38 +0100 Subject: [PATCH 67/82] Bump versions --- CHANGELOG.md | 8 +++++++- nextflow.config | 2 +- tests/default.nf.test.snap | 4 ++-- tests/featurecounts_group_type.nf.test.snap | 4 ++-- tests/hisat2.nf.test.snap | 4 ++-- tests/kallisto.nf.test.snap | 4 ++-- tests/min_mapped_reads.nf.test.snap | 4 ++-- tests/remove_ribo_rna.nf.test.snap | 4 ++-- tests/salmon.nf.test.snap | 4 ++-- tests/skip_qc.nf.test.snap | 4 ++-- tests/skip_trimming.nf.test.snap | 2 +- tests/star_rsem.nf.test.snap | 4 ++-- workflows/rnaseq/assets/multiqc/multiqc_config.yml | 2 +- 13 files changed, 28 insertions(+), 22 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cacba7c82..c8b851c80 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev +## [[3.17.0](https://github.com/nf-core/rnaseq/releases/tag/3.17.0)] - 2024-10-23 ### Credits +Special thanks to the following for their contributions to the release: + +- [Maxime Garcia](https://github.com/maxulysse) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Pablo Gonzalez de Aledo](https://github.com/pabloaledo) + ### Enhancements & fixes - [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release diff --git a/nextflow.config b/nextflow.config index ada872ed7..468792d0f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -328,7 +328,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '3.17.0dev' + version = '3.17.0' doi = 'https://doi.org/10.5281/zenodo.1400710' } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b70ad3971..4165436ac 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -227,7 +227,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index bbe39ddd6..dfd3f3d2c 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -221,7 +221,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 78d8c3ad4..4b39b7703 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -44,7 +44,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -224,7 +224,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 8aea96806..8bd57f925 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -56,7 +56,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -294,7 +294,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index e11236066..bc6454c98 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1221,7 +1221,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 79b4954b9..0a379aea9 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -140,7 +140,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1435,7 +1435,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index aa517a395..1e6827546 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -50,7 +50,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -367,7 +367,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 0589bb509..a07a6dd43 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -40,7 +40,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -169,7 +169,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 56f9b6eba..a0bfa97e4 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -130,7 +130,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index c396c1a4a..31e9150d8 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -134,7 +134,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ @@ -1314,7 +1314,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/rnaseq": "v3.17.0dev" + "nf-core/rnaseq": "v3.17.0" } }, [ diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml index 9b8ee731a..08360f58c 100644 --- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml +++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: # Important checks and failures sample-status: From 62f4ffea34daf585de223d119de79e1e91391141 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 23 Oct 2024 14:33:40 +0100 Subject: [PATCH 68/82] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c8b851c80..d22b296bf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ Special thanks to the following for their contributions to the release: - [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build - [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility - [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility +- [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From 2a509996eda50fd6985e0134b1b8b47639c7bfcb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 16:54:24 +0200 Subject: [PATCH 69/82] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d22b296bf..51374d1e8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ Special thanks to the following for their contributions to the release: - [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility - [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release +- [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From 4316615c4d2469af037bda35a09706cd98613774 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 16:55:40 +0200 Subject: [PATCH 70/82] update and patch modules --- modules.json | 9 +- .../genomecov/bedtools-genomecov.diff | 35 ++++++++ modules/nf-core/bedtools/genomecov/main.nf | 2 +- modules/nf-core/cat/fastq/cat-fastq.diff | 35 ++++++++ modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/sortmerna/main.nf | 2 +- modules/nf-core/sortmerna/sortmerna.diff | 90 +++++++++++++------ modules/nf-core/star/align/main.nf | 2 +- modules/nf-core/star/align/star-align.diff | 38 ++++++++ modules/nf-core/star/genomegenerate/main.nf | 2 +- .../genomegenerate/star-genomegenerate.diff | 34 +++++++ 11 files changed, 218 insertions(+), 33 deletions(-) create mode 100644 modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff create mode 100644 modules/nf-core/cat/fastq/cat-fastq.diff create mode 100644 modules/nf-core/star/align/star-align.diff create mode 100644 modules/nf-core/star/genomegenerate/star-genomegenerate.diff diff --git a/modules.json b/modules.json index 61692d607..9667d1b6b 100644 --- a/modules.json +++ b/modules.json @@ -24,7 +24,8 @@ "cat/fastq": { "branch": "master", "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", - "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"], + "patch": "modules/nf-core/cat/fastq/cat-fastq.diff" }, "custom/catadditionalfasta": { "branch": "master", @@ -221,12 +222,14 @@ "star/align": { "branch": "master", "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/star/align/star-align.diff" }, "star/genomegenerate": { "branch": "master", "git_sha": "a5ad53288c79fa52c5ae708c317e09ec2dd149ab", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/star/genomegenerate/star-genomegenerate.diff" }, "stringtie/stringtie": { "branch": "master", diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff new file mode 100644 index 000000000..bb848b16f --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -0,0 +1,35 @@ +Changes in module 'nf-core/bedtools/genomecov' +Changes in 'bedtools/genomecov/main.nf': +--- modules/nf-core/bedtools/genomecov/main.nf ++++ modules/nf-core/bedtools/genomecov/main.nf +@@ -5,7 +5,7 @@ + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': +- 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" ++ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" + + input: + tuple val(meta), path(intervals), val(scale) + +'modules/nf-core/bedtools/genomecov/meta.yml' is unchanged +'modules/nf-core/bedtools/genomecov/environment.yml' is unchanged +'modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap' is unchanged +'modules/nf-core/bedtools/genomecov/tests/nextflow.config' is unchanged +Changes in 'bedtools/genomecov/tests/main.nf.test': +--- modules/nf-core/bedtools/genomecov/tests/main.nf.test ++++ modules/nf-core/bedtools/genomecov/tests/main.nf.test +@@ -3,11 +3,6 @@ + script "../main.nf" + process "BEDTOOLS_GENOMECOV" + config "./nextflow.config" +- +- tag "modules" +- tag "modules_nfcore" +- tag "bedtools" +- tag "bedtools/genomecov" + + test("sarscov2 - no scale") { + when { + +************************************************************ diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 35e2ab14b..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -5,7 +5,7 @@ process BEDTOOLS_GENOMECOV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" + 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/cat/fastq/cat-fastq.diff b/modules/nf-core/cat/fastq/cat-fastq.diff new file mode 100644 index 000000000..debb8944b --- /dev/null +++ b/modules/nf-core/cat/fastq/cat-fastq.diff @@ -0,0 +1,35 @@ +Changes in module 'nf-core/cat/fastq' +'modules/nf-core/cat/fastq/nextflow.config' was created +Changes in 'cat/fastq/main.nf': +--- modules/nf-core/cat/fastq/main.nf ++++ modules/nf-core/cat/fastq/main.nf +@@ -5,7 +5,7 @@ + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : +- 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" ++ 'nf-core/coreutils:9.5--ae99c88a9b28c264' }" + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + +'modules/nf-core/cat/fastq/meta.yml' is unchanged +'modules/nf-core/cat/fastq/environment.yml' is unchanged +'modules/nf-core/cat/fastq/tests/main.nf.test.snap' is unchanged +Changes in 'cat/fastq/tests/main.nf.test': +--- modules/nf-core/cat/fastq/tests/main.nf.test ++++ modules/nf-core/cat/fastq/tests/main.nf.test +@@ -5,10 +5,6 @@ + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" +- tag "modules" +- tag "modules_nfcore" +- tag "cat" +- tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + +'modules/nf-core/cat/fastq/tests/tags.yml' was removed +************************************************************ diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 4364a389b..f2848aa6e 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -5,7 +5,7 @@ process CAT_FASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : - 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" + 'nf-core/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index 6850dc1d7..b479f0459 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -5,7 +5,7 @@ process SORTMERNA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : - 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' }" + 'nf-core/sortmerna:4.3.7--6502243397c065ba' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sortmerna/sortmerna.diff b/modules/nf-core/sortmerna/sortmerna.diff index 5c3b1775d..187650b2a 100644 --- a/modules/nf-core/sortmerna/sortmerna.diff +++ b/modules/nf-core/sortmerna/sortmerna.diff @@ -1,4 +1,5 @@ Changes in module 'nf-core/sortmerna' +'modules/nf-core/sortmerna/nextflow.config' was created Changes in 'sortmerna/main.nf': --- modules/nf-core/sortmerna/main.nf +++ modules/nf-core/sortmerna/main.nf @@ -9,11 +10,12 @@ Changes in 'sortmerna/main.nf': - 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : - 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : -+ 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' }" ++ 'nf-core/sortmerna:4.3.7--6502243397c065ba' }" input: tuple val(meta), path(reads) +'modules/nf-core/sortmerna/meta.yml' is unchanged Changes in 'sortmerna/environment.yml': --- modules/nf-core/sortmerna/environment.yml +++ modules/nf-core/sortmerna/environment.yml @@ -24,8 +26,6 @@ Changes in 'sortmerna/environment.yml': - - bioconda::sortmerna=4.3.6 + - seqera::sortmerna=4.3.7 -'modules/nf-core/sortmerna/meta.yml' is unchanged -'modules/nf-core/sortmerna/nextflow.config' was created Changes in 'sortmerna/tests/main.nf.test.snap': --- modules/nf-core/sortmerna/tests/main.nf.test.snap +++ modules/nf-core/sortmerna/tests/main.nf.test.snap @@ -174,15 +174,15 @@ Changes in 'sortmerna/tests/main.nf.test.snap': - }, - "timestamp": "2024-02-26T15:01:53.832643452" + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", -+ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", -+ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, -+ "timestamp": "2024-10-22T10:40:14.159307146" ++ "timestamp": "2024-10-22T12:02:37.578808801" }, "versions_single_end_premade_index": { "content": [ @@ -208,8 +208,8 @@ Changes in 'sortmerna/tests/main.nf.test.snap': + "content": [ + [ + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", -+ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", -+ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" + ], + [ + "versions.yml:md5,1ba8f45ec168b6ebfceb9d4a4203f655" @@ -219,7 +219,7 @@ Changes in 'sortmerna/tests/main.nf.test.snap': + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, -+ "timestamp": "2024-10-22T10:38:39.794977786" ++ "timestamp": "2024-10-22T11:59:11.705138075" }, "sarscov2 paired_end-for_stub_match": { "content": [ @@ -258,15 +258,15 @@ Changes in 'sortmerna/tests/main.nf.test.snap': - }, - "timestamp": "2024-02-26T14:24:14.272659781" + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", -+ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", -+ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, -+ "timestamp": "2024-10-22T10:39:48.72523749" ++ "timestamp": "2024-10-22T12:01:29.664107565" }, "sarscov2 single_end_premade_index_match_stub": { "content": [ @@ -463,15 +463,15 @@ Changes in 'sortmerna/tests/main.nf.test.snap': - }, - "timestamp": "2024-02-26T15:00:35.34089252" + "2415186086593376314.bursttrie_0.dat:md5,74f7f020e8d46e24a8a2e9c5fbcd564a", -+ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef", -+ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7" ++ "2415186086593376314.kmer_0.dat:md5,4a0bcb71b120f6a6949b7969292ef2e7", ++ "2415186086593376314.pos_0.dat:md5,bc2875e4cc4017707306565e396839ef" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, -+ "timestamp": "2024-10-22T10:39:09.050777261" ++ "timestamp": "2024-10-22T12:00:30.580004574" }, "sarscov2 single_end_premade_index_match": { "content": [ @@ -492,48 +492,88 @@ Changes in 'sortmerna/tests/main.nf.test.snap': Changes in 'sortmerna/tests/main.nf.test': --- modules/nf-core/sortmerna/tests/main.nf.test +++ modules/nf-core/sortmerna/tests/main.nf.test -@@ -27,8 +27,10 @@ +@@ -24,11 +24,17 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ assertAll( { assert process.success }, { assert ! process.out.reads }, - { assert snapshot(process.out.index).match("index_index_only") }, - { assert snapshot(process.out.versions).match("versions_index_only") } + { assert snapshot( -+ file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }, ++ index_files, + process.out.versions + ).match() }, ) } -@@ -92,7 +94,7 @@ +@@ -79,6 +85,10 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert process.out.reads }, +@@ -92,7 +102,7 @@ ).sort() ).match("sarscov2 single_end_match") }, - { assert snapshot(process.out.index).match("index_single_end") }, -+ { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_single_end") }, ++ { assert snapshot(index_files).match("index_single_end") }, { assert snapshot(process.out.versions).match("versions_single_end") } ) } -@@ -170,7 +172,7 @@ +@@ -157,6 +167,10 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert process.out.reads }, +@@ -170,7 +184,7 @@ ).sort() ).match("sarscov2 paired_end_match") }, - { assert snapshot(process.out.index).match("index_paired_end") }, -+ { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats")}).match("index_paired_end") }, ++ { assert snapshot(index_files).match("index_paired_end") }, { assert snapshot(process.out.versions).match("versions_paired_end") } ) } -@@ -265,7 +267,7 @@ +@@ -252,6 +266,10 @@ + } + + then { ++ def index_files = file(process.out.index[0][1]).listFiles() ++ .findAll { !it.name.endsWith('.stats') } ++ .sort { a, b -> a.name <=> b.name } ++ + assertAll( + { assert process.success }, + { assert process.out.reads }, +@@ -265,7 +283,7 @@ ).sort() ).match("sarscov2 single_end_premade_index_match") }, - { assert snapshot(process.out.index).match("index_single_end_premade_index") }, -+ { assert snapshot(file(process.out.index[0][1]).listFiles().findAll { !it.name.endsWith(".stats") }).match("index_single_end_premade_index") }, ++ { assert snapshot(index_files).match("index_single_end_premade_index") }, { assert snapshot(process.out.versions).match("versions_single_end_premade_index") } ) } -'modules/nf-core/sortmerna/tests/tags.yml' is unchanged -'modules/nf-core/sortmerna/tests/premade_index.config' is unchanged 'modules/nf-core/sortmerna/tests/indexing_only.config' is unchanged +'modules/nf-core/sortmerna/tests/premade_index.config' is unchanged +'modules/nf-core/sortmerna/tests/tags.yml' was removed ************************************************************ diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 417071ba9..b5d2fbd58 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -5,7 +5,7 @@ process STAR_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" + 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/star-align.diff b/modules/nf-core/star/align/star-align.diff new file mode 100644 index 000000000..84e65ca00 --- /dev/null +++ b/modules/nf-core/star/align/star-align.diff @@ -0,0 +1,38 @@ +Changes in module 'nf-core/star/align' +Changes in 'star/align/main.nf': +--- modules/nf-core/star/align/main.nf ++++ modules/nf-core/star/align/main.nf +@@ -5,7 +5,7 @@ + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + +'modules/nf-core/star/align/meta.yml' is unchanged +'modules/nf-core/star/align/environment.yml' is unchanged +'modules/nf-core/star/align/tests/main.nf.test.snap' is unchanged +'modules/nf-core/star/align/tests/nextflow.config' is unchanged +'modules/nf-core/star/align/tests/nextflow.starfusion.config' is unchanged +'modules/nf-core/star/align/tests/nextflow.arriba.config' is unchanged +Changes in 'star/align/tests/main.nf.test': +--- modules/nf-core/star/align/tests/main.nf.test ++++ modules/nf-core/star/align/tests/main.nf.test +@@ -3,11 +3,6 @@ + name "Test Process STAR_ALIGN" + script "../main.nf" + process "STAR_ALIGN" +- tag "modules" +- tag "modules_nfcore" +- tag "star" +- tag "star/align" +- tag "star/genomegenerate" + + test("homo_sapiens - single_end") { + config "./nextflow.config" + +'modules/nf-core/star/align/tests/tags.yml' was removed +************************************************************ diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 8f0c67e76..bdd1d0db0 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -5,7 +5,7 @@ process STAR_GENOMEGENERATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" + 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff new file mode 100644 index 000000000..515dd1bac --- /dev/null +++ b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff @@ -0,0 +1,34 @@ +Changes in module 'nf-core/star/genomegenerate' +Changes in 'star/genomegenerate/main.nf': +--- modules/nf-core/star/genomegenerate/main.nf ++++ modules/nf-core/star/genomegenerate/main.nf +@@ -5,7 +5,7 @@ + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" + + input: + tuple val(meta), path(fasta) + +'modules/nf-core/star/genomegenerate/meta.yml' is unchanged +'modules/nf-core/star/genomegenerate/environment.yml' is unchanged +'modules/nf-core/star/genomegenerate/tests/main.nf.test.snap' is unchanged +Changes in 'star/genomegenerate/tests/main.nf.test': +--- modules/nf-core/star/genomegenerate/tests/main.nf.test ++++ modules/nf-core/star/genomegenerate/tests/main.nf.test +@@ -3,10 +3,6 @@ + name "Test Process STAR_GENOMEGENERATE" + script "../main.nf" + process "STAR_GENOMEGENERATE" +- tag "modules" +- tag "modules_nfcore" +- tag "star" +- tag "star/genomegenerate" + + test("fasta_gtf") { + + +'modules/nf-core/star/genomegenerate/tests/tags.yml' was removed +************************************************************ From e94558ba2819f347699d3b3fedffe40fa0f89f87 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:23:46 +0200 Subject: [PATCH 71/82] update CHANGELOG --- CHANGELOG.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 51374d1e8..c3011a087 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,37 @@ Special thanks to the following for their contributions to the release: - [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies + +### Software dependencies + +| Dependency | Old version | New version | +| ----------------------------- | ----------- | ----------- | +| `bbmap` | 39.01 | 39.10 | +| `coreutils` | 8.30 | 9.5 | +| `fq` | 0.9.1 | 0.12.0 | +| `python (catadditionalfasta)` | 3.9.5 | 3.12.2 | +| `python (tx2gene)` | 3.9.5 | 3.10.4 | +| `cutadapt` | 3.4 | 4.9 | +| `htslib (star)` | 1.18 | 1.20 | +| `htslib` | 1.20 | 1.21 | +| `kallisto` | 0.48.0 | 0.51.1 | +| `preseq` | 3.1.2 | 3.2.0 | +| `salmon` | 1.10.1 | 1.10.3 | +| `samtools (star)` | 1.18 | 1.20 | +| `samtools` | 1.20 | 1.21 | +| `sortmerna` | 4.3.6 | 4.3.7 | +| `star` | 2.7.10a | =2.7.11b | +| `stringtie` | 2.2.1 | 2.2.3 | +| `subread` | 2.0.1 | 2.0.6 | +| `trim-galore` | 0.6.7 | 0.6.10 | +| `ucsc-bedgraphtobigwig` | 445 | 469 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From b5f530fc8fa20fcbe6c7eb3a4ffbd64eb2f53bf5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:28:19 +0200 Subject: [PATCH 72/82] fix CI --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6346287ac..a02a316a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,7 +44,7 @@ jobs: test: name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" needs: [nf-test-changes] - if: needs.nf-test-changes.outputs.nf_test_files != '[]' + if: nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false From 97d3697b36ba84f399b4c76b4f07b72c0ea35d7d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:29:21 +0200 Subject: [PATCH 73/82] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3011a087..abc9cd032 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ Special thanks to the following for their contributions to the release: - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Fix CI triggers ### Software dependencies From 23d3ee75a7a8c8753b441b9b9034391784aa6b6e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:31:26 +0200 Subject: [PATCH 74/82] fix GHA --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a02a316a5..40125fbb2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,7 +44,6 @@ jobs: test: name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" needs: [nf-test-changes] - if: nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false From b55c81a42af1788920e0405e4cf8a9ca9d399832 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:35:20 +0200 Subject: [PATCH 75/82] revert GHA --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 40125fbb2..6346287ac 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,6 +44,7 @@ jobs: test: name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" needs: [nf-test-changes] + if: needs.nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false From 9690d295a68dca62217409ff266fa719a062f8ac Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:35:33 +0200 Subject: [PATCH 76/82] revert CHANGELOG --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index abc9cd032..c3011a087 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,6 @@ Special thanks to the following for their contributions to the release: - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies -- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Fix CI triggers ### Software dependencies From ac1b7e08517665e0f8b372ee4912056858a79831 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 20:42:58 +0200 Subject: [PATCH 77/82] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3011a087..fc825f839 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ Special thanks to the following for their contributions to the release: - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix ### Software dependencies From 38903446cbfeed8d1dd62b8780cbf86cc2df5515 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 20:43:07 +0200 Subject: [PATCH 78/82] remove conda from matrix --- .github/workflows/ci.yml | 38 -------------------------------------- 1 file changed, 38 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6346287ac..3660947b7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,37 +54,14 @@ jobs: - "latest-everything" nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - - "conda" - "docker" - "singularity" isMaster: - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev exclude: - - isMaster: false - profile: "conda" - isMaster: false profile: "singularity" - - profile: "conda" - nf_test_files: "tests/default.nf.test" - - profile: "conda" - nf_test_files: "tests/featurecounts_group_type.nf.test" - - profile: "conda" - nf_test_files: "tests/hisat2.nf.test" - - profile: "conda" - nf_test_files: "tests/kallisto.nf.test" - - profile: "conda" - nf_test_files: "tests/min_mapped_reads.nf.test" - - profile: "conda" - nf_test_files: "tests/remove_ribo_rna.nf.test" - - profile: "conda" - nf_test_files: "tests/salmon.nf.test" - - profile: "conda" - nf_test_files: "tests/skip_qc.nf.test" - - profile: "conda" - nf_test_files: "tests/skip_trimming.nf.test" - - profile: "conda" - nf_test_files: "tests/star_rsem.nf.test" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -104,21 +81,6 @@ jobs: mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - name: Install nf-test uses: nf-core/setup-nf-test@v1 with: From a0ee0b3a3d54c4bba134b1ee706044af5755b623 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Oct 2024 09:39:42 +0200 Subject: [PATCH 79/82] further reduce down the matrix --- .github/workflows/ci.yml | 2 ++ CHANGELOG.md | 1 + 2 files changed, 3 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3660947b7..2f4646244 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -62,6 +62,8 @@ jobs: exclude: - isMaster: false profile: "singularity" + - NXF_VER: "latest-everything" + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 diff --git a/CHANGELOG.md b/CHANGELOG.md index fc825f839..a90687383 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ Special thanks to the following for their contributions to the release: - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix +- [PR #1439](https://github.com/nf-core/rnaseq/pull/1439) - Further reduce matrix ### Software dependencies From b78e15af4d17872d79e6c8cc977cc39957e5e007 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Oct 2024 09:41:32 +0200 Subject: [PATCH 80/82] update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a90687383..d87588c9c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,7 +24,7 @@ Special thanks to the following for their contributions to the release: - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix -- [PR #1439](https://github.com/nf-core/rnaseq/pull/1439) - Further reduce matrix +- [PR #1440](https://github.com/nf-core/rnaseq/pull/1440) - Further reduce matrix ### Software dependencies From 14e76774942a3fe4c9837541af5edb8457cc640c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Oct 2024 09:48:38 +0200 Subject: [PATCH 81/82] force convert for some singularity images --- .../nf-core/bedtools/genomecov/bedtools-genomecov.diff | 10 ++++++---- modules/nf-core/bedtools/genomecov/main.nf | 4 +--- modules/nf-core/cat/fastq/cat-fastq.diff | 10 ++++++---- modules/nf-core/cat/fastq/main.nf | 4 +--- modules/nf-core/sortmerna/main.nf | 4 +--- modules/nf-core/sortmerna/sortmerna.diff | 8 ++++---- modules/nf-core/star/align/main.nf | 4 +--- modules/nf-core/star/align/star-align.diff | 10 ++++++---- modules/nf-core/star/genomegenerate/main.nf | 4 +--- .../star/genomegenerate/star-genomegenerate.diff | 10 ++++++---- 10 files changed, 33 insertions(+), 35 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index bb848b16f..17aa9eb2d 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -2,12 +2,14 @@ Changes in module 'nf-core/bedtools/genomecov' Changes in 'bedtools/genomecov/main.nf': --- modules/nf-core/bedtools/genomecov/main.nf +++ modules/nf-core/bedtools/genomecov/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_single' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" ++ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 91869ec23..10a99d439 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,9 +3,7 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" + container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/cat/fastq/cat-fastq.diff b/modules/nf-core/cat/fastq/cat-fastq.diff index debb8944b..0d3832c04 100644 --- a/modules/nf-core/cat/fastq/cat-fastq.diff +++ b/modules/nf-core/cat/fastq/cat-fastq.diff @@ -3,12 +3,14 @@ Changes in module 'nf-core/cat/fastq' Changes in 'cat/fastq/main.nf': --- modules/nf-core/cat/fastq/main.nf +++ modules/nf-core/cat/fastq/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_single' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : - 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" -+ 'nf-core/coreutils:9.5--ae99c88a9b28c264' }" ++ container 'nf-core/coreutils:9.5--ae99c88a9b28c264' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index f2848aa6e..6f4f96e34 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,9 +3,7 @@ process CAT_FASTQ { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : - 'nf-core/coreutils:9.5--ae99c88a9b28c264' }" + container 'nf-core/coreutils:9.5--ae99c88a9b28c264' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index b479f0459..2ea221c59 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,9 +3,7 @@ process SORTMERNA { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : - 'nf-core/sortmerna:4.3.7--6502243397c065ba' }" + container 'nf-core/sortmerna:4.3.7--6502243397c065ba' input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sortmerna/sortmerna.diff b/modules/nf-core/sortmerna/sortmerna.diff index 187650b2a..5e37cabf8 100644 --- a/modules/nf-core/sortmerna/sortmerna.diff +++ b/modules/nf-core/sortmerna/sortmerna.diff @@ -3,14 +3,14 @@ Changes in module 'nf-core/sortmerna' Changes in 'sortmerna/main.nf': --- modules/nf-core/sortmerna/main.nf +++ modules/nf-core/sortmerna/main.nf -@@ -4,8 +4,8 @@ +@@ -3,9 +3,7 @@ + label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : - 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : -+ 'nf-core/sortmerna:4.3.7--6502243397c065ba' }" ++ container 'nf-core/sortmerna:4.3.7--6502243397c065ba' input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index b5d2fbd58..eadddb03f 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,9 +3,7 @@ process STAR_ALIGN { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" + container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/star-align.diff b/modules/nf-core/star/align/star-align.diff index 84e65ca00..ea28fb1aa 100644 --- a/modules/nf-core/star/align/star-align.diff +++ b/modules/nf-core/star/align/star-align.diff @@ -2,12 +2,14 @@ Changes in module 'nf-core/star/align' Changes in 'star/align/main.nf': --- modules/nf-core/star/align/main.nf +++ modules/nf-core/star/align/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_high' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" -+ 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index bdd1d0db0..af72f920b 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,9 +3,7 @@ process STAR_GENOMEGENERATE { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" + container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff index 515dd1bac..dea48619b 100644 --- a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff +++ b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff @@ -2,12 +2,14 @@ Changes in module 'nf-core/star/genomegenerate' Changes in 'star/genomegenerate/main.nf': --- modules/nf-core/star/genomegenerate/main.nf +++ modules/nf-core/star/genomegenerate/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_high' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" -+ 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(fasta) From cb5cc2c3f035dddf9b54ac22ca38bcf1a2475365 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Oct 2024 10:16:20 +0200 Subject: [PATCH 82/82] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d87588c9c..39e77a767 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ Special thanks to the following for their contributions to the release: - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix - [PR #1440](https://github.com/nf-core/rnaseq/pull/1440) - Further reduce matrix +- [PR #1441](https://github.com/nf-core/rnaseq/pull/1441) - Force some containers to be converted from docker to singularity to fix nf-core download tests ### Software dependencies