diff --git a/CHANGELOG.md b/CHANGELOG.md index ec6d5c24..1d6176c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,7 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz` - [[#429]](https://github.com/nf-core/smrnaseq/pull/429) - Make [saving of intermediate files optional](https://github.com/nf-core/smrnaseq/issues/424) - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as `params.save_aligned` and `params.save_aligned_mirna_quant`. - [[#433]](https://github.com/nf-core/smrnaseq/pull/433) - Replace local instances of bowtie for nf-core [`bowtie2`](https://github.com/nf-core/smrnaseq/issues/434) and [`bowtie1`](https://github.com/nf-core/smrnaseq/issues/433) - Additionally adds a `bioawk` module that cleans fasta files. -- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC. +- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC and all modules to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC. +- [[#435]](https://github.com/nf-core/smrnaseq/pull/435) - Update [Mirtop to latest version](https://github.com/nf-core/smrnaseq/issues/437) - Process samples separately and join results with `CSVTK_JOIN`. ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch diff --git a/conf/modules.config b/conf/modules.config index 540f8426..de9f4ace 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -370,14 +370,30 @@ process { ] } - withName: 'MIRTOP_COUNTS' { + withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_COUNTS' { ext.args = '--add-extra' + publishDir = [ enabled: false ] + } + + withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_STATS' { + publishDir = [ enabled: false ] } - withName: 'MIRTOP_GFF' { + withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:BAM_STATS_MIRNA_MIRTOP:MIRTOP_GFF' { publishDir = [ path: { "${params.outdir}/mirna_quant/mirtop/gff" }, mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:CSVTK_JOIN' { + ext.args = "--fields 'UID,Read,miRNA,Variant,iso_5p,iso_3p,iso_add3p,iso_snp,iso_5p_nt,iso_3p_nt,iso_add3p_nt,iso_snp_nt' --tabs --outer-join --na \"0\" --out-delimiter \"\t\"" + ext.prefix = "joined_samples_mirtop" + publishDir = [ + path: { "${params.outdir}/mirna_quant/mirtop" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } diff --git a/docs/output.md b/docs/output.md index 0fdba8f9..334d2c1b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -140,9 +140,9 @@ If `--save_intermediates` is specified, these files will be placed in this direc **Output directory: `results/mirtop`** -- `mirtop.gff`: [mirgff3](https://github.com/miRTop/mirGFF3) file -- `mirtop.tsv`: tabular file of the previous file for easy integration with downstream analysis. -- `mirtop_rawData.tsv`: File compatible with [isomiRs](http://lpantano.github.io/isomiRs/reference/IsomirDataSeqFromMirtop.html) Bioconductor package to perform isomiRs analysis. +- `gff/{sample.id}.gff`: [mirgff3](https://github.com/miRTop/mirGFF3) file +- `joined_samples_mirtop.tsv`: tabular file of the previous file for easy integration with downstream analysis. +- `export/{sample.id}_mirtop_rawData.tsv`: File compatible with [isomiRs](http://lpantano.github.io/isomiRs/reference/IsomirDataSeqFromMirtop.html) Bioconductor package to perform isomiRs analysis. - `mirna.tsv`: tabular file with miRNA counts after summarizing unique isomiRs for each miRNA ## miRDeep2 diff --git a/modules.json b/modules.json index 4f6a5c98..84c3771f 100644 --- a/modules.json +++ b/modules.json @@ -36,6 +36,11 @@ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, + "csvtk/join": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, "fastp": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", @@ -53,22 +58,22 @@ }, "mirtop/counts": { "branch": "master", - "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721", + "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d", "installed_by": ["bam_stats_mirna_mirtop"] }, "mirtop/export": { "branch": "master", - "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721", + "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d", "installed_by": ["bam_stats_mirna_mirtop"] }, "mirtop/gff": { "branch": "master", - "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721", + "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d", "installed_by": ["bam_stats_mirna_mirtop"] }, "mirtop/stats": { "branch": "master", - "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721", + "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d", "installed_by": ["bam_stats_mirna_mirtop"] }, "mirtrace/qc": { @@ -148,7 +153,7 @@ }, "bam_stats_mirna_mirtop": { "branch": "master", - "git_sha": "43b2b702abd8ab2cb1aa1365763f518413ad5721", + "git_sha": "196062335bb9ec979075bf2212f64a369b927b0d", "installed_by": ["subworkflows"] }, "bam_stats_samtools": { diff --git a/modules/local/datatable_merge/datatable_merge.nf b/modules/local/datatable_merge/datatable_merge.nf index fcfed309..ef1afc05 100644 --- a/modules/local/datatable_merge/datatable_merge.nf +++ b/modules/local/datatable_merge/datatable_merge.nf @@ -7,7 +7,7 @@ process TABLE_MERGE { 'biocontainers/r-data.table:1.12.2' }" input: - path mirtop + tuple val(meta), path(mirtop) output: path "mirna.tsv" , emit: mirna_tsv diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml new file mode 100644 index 00000000..ea951bdb --- /dev/null +++ b/modules/nf-core/csvtk/join/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::csvtk=0.30.0 diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf new file mode 100644 index 00000000..5f3afeea --- /dev/null +++ b/modules/nf-core/csvtk/join/main.nf @@ -0,0 +1,49 @@ +process CSVTK_JOIN { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/csvtk:0.30.0--h9ee0642_0': + 'biocontainers/csvtk:0.30.0--h9ee0642_0' }" + + input: + tuple val(meta), path(csv) + + output: + tuple val(meta), path("${prefix}.${out_extension}"), emit: csv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv" + """ + csvtk \\ + join \\ + $args \\ + --num-cpus $task.cpus \\ + --out-file ${prefix}.${out_extension} \\ + $csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" )) + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv" + """ + touch ${prefix}.${out_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" )) + END_VERSIONS + """ +} diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml new file mode 100644 index 00000000..d8671b17 --- /dev/null +++ b/modules/nf-core/csvtk/join/meta.yml @@ -0,0 +1,45 @@ +name: csvtk_join +description: Join two or more CSV (or TSV) tables by selected fields into a single + table +keywords: + - join + - tsv + - csv +tools: + - csvtk: + description: A cross-platform, efficient, practical CSV/TSV toolkit + homepage: http://bioinf.shenwei.me/csvtk + documentation: http://bioinf.shenwei.me/csvtk + tool_dev_url: https://github.com/shenwei356/csvtk + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV formatted files + pattern: "*.{csv,tsv}" +output: + - csv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${out_extension}: + type: file + description: Joined CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "version.yml" +authors: + - "@anoronh4" +maintainers: + - "@anoronh4" diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test b/modules/nf-core/csvtk/join/tests/main.nf.test new file mode 100644 index 00000000..3cf178c4 --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/main.nf.test @@ -0,0 +1,64 @@ +nextflow_process { + + name "Test Process CSVTK_JOIN" + script "../main.nf" + process "CSVTK_JOIN" + + tag "modules" + tag "modules_nfcore" + tag "csvtk" + tag "csvtk/join" + + test("join - csv") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_short.csv", checkIfExists: true), + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("join - csv - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_short.csv", checkIfExists: true), + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test.snap b/modules/nf-core/csvtk/join/tests/main.nf.test.snap new file mode 100644 index 00000000..b124788b --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "join - csv": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d0ad82ca096c7e05eb9f9a04194c9e30" + ] + ], + "1": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d0ad82ca096c7e05eb9f9a04194c9e30" + ] + ], + "versions": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ] + } + ], + "timestamp": "2024-05-21T15:45:44.045434" + }, + "join - csv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ] + } + ], + "timestamp": "2024-05-21T15:45:55.59201" + } +} \ No newline at end of file diff --git a/modules/nf-core/csvtk/join/tests/nextflow.config b/modules/nf-core/csvtk/join/tests/nextflow.config new file mode 100644 index 00000000..1b14393a --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: CSVTK_JOIN { + ext.args = "--fields 'ID;ID' -p -e -d \"\t\" -D \",\"" + } +} diff --git a/modules/nf-core/csvtk/join/tests/tags.yml b/modules/nf-core/csvtk/join/tests/tags.yml new file mode 100644 index 00000000..6c3a0fa6 --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/tags.yml @@ -0,0 +1,2 @@ +csvtk/join: + - "modules/nf-core/csvtk/join/**" diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml index ed1198d8..1f5deb37 100644 --- a/modules/nf-core/mirtop/counts/environment.yml +++ b/modules/nf-core/mirtop/counts/environment.yml @@ -4,6 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "conda-forge::r-base=4.1.1" - - "conda-forge::r-data.table=1.14.2" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf index 9b623bff..a4ca1889 100644 --- a/modules/nf-core/mirtop/counts/main.nf +++ b/modules/nf-core/mirtop/counts/main.nf @@ -3,9 +3,7 @@ process MIRTOP_COUNTS { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/counts/meta.yml b/modules/nf-core/mirtop/counts/meta.yml index 904dbd31..679df7b0 100644 --- a/modules/nf-core/mirtop/counts/meta.yml +++ b/modules/nf-core/mirtop/counts/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_counts" -description: mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples. +description: mirtop counts generates a file with the minimal information about each + sequence and the count data in columns for each samples. keywords: - mirna - isomir @@ -13,44 +13,55 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - counts/*.tsv: + type: file + description: TSV file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test index 52b31db1..5048c166 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test @@ -54,12 +54,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.versions - ).match() - }, - // md5sum is not stable, order of elements in column "variant" change - { assert file(process.out.tsv[0][1]).readLines().findAll { it.contains("iso-22-I0S21NSLN") }} + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap index d05798b0..104acf13 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" ], "tsv": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" ] } ], @@ -30,18 +30,39 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T13:24:41.148536938" + "timestamp": "2024-09-18T15:05:22.556134542" }, "isomir - bam": { "content": [ - [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" - ] + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6" + ] + ], + "1": [ + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" + ], + "tsv": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6" + ] + ], + "versions": [ + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" + ] + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T18:39:50.607483472" + "timestamp": "2024-09-18T16:05:58.332523272" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml index 4b5ae03a..17572707 100644 --- a/modules/nf-core/mirtop/export/environment.yml +++ b/modules/nf-core/mirtop/export/environment.yml @@ -1,10 +1,11 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "bioconda::samtools=1.15.1" - - "conda-forge::r-base=4.1.1" - - "conda-forge::r-data.table=1.14.2" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/export/main.nf b/modules/nf-core/mirtop/export/main.nf index 33f6c303..b99333de 100644 --- a/modules/nf-core/mirtop/export/main.nf +++ b/modules/nf-core/mirtop/export/main.nf @@ -3,9 +3,7 @@ process MIRTOP_EXPORT { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/export/meta.yml b/modules/nf-core/mirtop/export/meta.yml index d797f783..25f66c3b 100644 --- a/modules/nf-core/mirtop/export/meta.yml +++ b/modules/nf-core/mirtop/export/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_export" -description: mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package +description: mirtop export generates files such as fasta, vcf or compatible with isomiRs + bioconductor package keywords: - mirna - isomir @@ -13,52 +13,75 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*_rawData.tsv: + type: file + description: TSV file + pattern: "*.{tsv}" - fasta: - type: file - description: FASTA file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*.fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa}" - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*.vcf*: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap index f8c668a6..ea272199 100644 --- a/modules/nf-core/mirtop/export/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/export/tests/main.nf.test.snap @@ -22,7 +22,7 @@ ] ], "3": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ], "fasta": [ [ @@ -44,7 +44,7 @@ ] ], "versions": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ] } ], @@ -52,7 +52,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T15:25:40.531010949" + "timestamp": "2024-09-18T14:54:17.653801164" }, "isomir - bam": { "content": [ @@ -72,7 +72,7 @@ ], "3": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ], "fasta": [ @@ -89,7 +89,7 @@ ], "versions": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ] } ], @@ -97,6 +97,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T23:12:49.612315132" + "timestamp": "2024-09-18T16:06:37.626754369" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/gff/environment.yml b/modules/nf-core/mirtop/gff/environment.yml index 6e57308a..1f5deb37 100644 --- a/modules/nf-core/mirtop/gff/environment.yml +++ b/modules/nf-core/mirtop/gff/environment.yml @@ -4,5 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "bioconda::samtools=1.15.1" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf index 453b624b..aeb26bcc 100644 --- a/modules/nf-core/mirtop/gff/main.nf +++ b/modules/nf-core/mirtop/gff/main.nf @@ -3,9 +3,7 @@ process MIRTOP_GFF { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(bam, arity:'1..*') @@ -14,7 +12,7 @@ process MIRTOP_GFF { output: tuple val(meta), path("mirtop/*mirtop.gff") , emit: gff - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mirtop/gff/meta.yml b/modules/nf-core/mirtop/gff/meta.yml index 454d5edf..8e23f054 100644 --- a/modules/nf-core/mirtop/gff/meta.yml +++ b/modules/nf-core/mirtop/gff/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_gff" description: mirtop gff generates the GFF3 adapter format to capture miRNA variations @@ -13,44 +12,55 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: GFF file - pattern: "*.{gff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop/*mirtop.gff: + type: file + description: GFF file + pattern: "*.{gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test index 3ce7ef85..85977b43 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test @@ -33,13 +33,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.bam, - process.out.versions, - ).match() - }, - // md5sum is not stable, order of elements in section "variant" may change - { assert file(process.out.gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }} + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap index a9e6f852..0dddae2d 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" ], "gff": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" ] } ], @@ -30,19 +30,39 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T22:40:30.542921953" + "timestamp": "2024-09-18T14:31:04.976117723" }, "isomir - bam": { "content": [ - null, - [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" - ] + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9" + ] + ], + "1": [ + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" + ], + "gff": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9" + ] + ], + "versions": [ + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" + ] + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T22:38:09.903017316" + "timestamp": "2024-09-18T16:07:04.203181613" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/stats/environment.yml b/modules/nf-core/mirtop/stats/environment.yml index 3c24c43e..1f5deb37 100644 --- a/modules/nf-core/mirtop/stats/environment.yml +++ b/modules/nf-core/mirtop/stats/environment.yml @@ -4,5 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "conda-forge::pandas=1.3.5" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/stats/main.nf b/modules/nf-core/mirtop/stats/main.nf index 51d33019..4742448b 100644 --- a/modules/nf-core/mirtop/stats/main.nf +++ b/modules/nf-core/mirtop/stats/main.nf @@ -4,9 +4,7 @@ process MIRTOP_STATS { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/stats/meta.yml b/modules/nf-core/mirtop/stats/meta.yml index 1bcd2248..ebce7d99 100644 --- a/modules/nf-core/mirtop/stats/meta.yml +++ b/modules/nf-core/mirtop/stats/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_stats" -description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category. +description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF + file by isomiR category. keywords: - mirna - isomir @@ -13,37 +13,44 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: Mirtop GFF file obtained with mirtop_gff - pattern: "*.{gff}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: Mirtop GFF file obtained with mirtop_gff + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: TXT file with stats - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - stats/*.txt: + type: file + description: TXT file with stats + pattern: "*.{txt}" - log: - type: file - description: log file with stats - pattern: "*.{log}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - stats/*_stats.log: + type: file + description: log file with stats + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap index ba9633d1..2904830d 100644 --- a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ], "log": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T17:49:32.73944037" + "timestamp": "2024-09-18T15:02:00.325615537" }, "isomir - bam": { "content": [ @@ -56,7 +56,7 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + "mirtop_stats.txt:md5,006f8767fe5afd6f66c83a28a1caba63" ] ], "1": [ @@ -64,18 +64,18 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + "mirtop_stats.log:md5,8fa28ad20bb1b1a91245f2c1e6613f85" ] ], "2": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ], "log": [ [ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + "mirtop_stats.log:md5,8fa28ad20bb1b1a91245f2c1e6613f85" ] ], "txt": [ @@ -83,11 +83,11 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + "mirtop_stats.txt:md5,006f8767fe5afd6f66c83a28a1caba63" ] ], "versions": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ] } ], @@ -95,6 +95,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T17:47:39.121648755" + "timestamp": "2024-09-18T15:01:49.621322368" } } \ No newline at end of file diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf index b9f6a542..c93a09ae 100644 --- a/subworkflows/local/mirna_quant.nf +++ b/subworkflows/local/mirna_quant.nf @@ -22,6 +22,7 @@ include { SEQCLUSTER_COLLAPSE } from '../../modules/nf-core/seqcluster/collapse include { TABLE_MERGE } from '../../modules/local/datatable_merge/datatable_merge.nf' include { EDGER_QC } from '../../modules/local/edger_qc/edger_qc.nf' include { BAM_STATS_MIRNA_MIRTOP } from '../../subworkflows/nf-core/bam_stats_mirna_mirtop/main' +include { CSVTK_JOIN } from '../../modules/nf-core/csvtk/join/main' workflow MIRNA_QUANT { take: @@ -97,24 +98,26 @@ workflow MIRNA_QUANT { // nf-core/mirtop - ch_bams = BOWTIE_MAP_SEQCLUSTER.out.bam - .collect{it[1]} - .map{it -> return [[id:"bams"], it]} - ch_mirna_gtf_species = ch_mirna_gtf .combine(ch_mirtrace_species) .map{ gtf, species -> [ [id:species.toString()], gtf, species ] } .collect() BAM_STATS_MIRNA_MIRTOP( - ch_bams, // TODO: Parallelize by running each BOWTIE_MAP_SEQCLUSTER.out.bam separately when mirtop solves this issue: https://github.com/miRTop/mirtop/issues/83 + BOWTIE_MAP_SEQCLUSTER.out.bam, FORMAT_HAIRPIN.out.formatted_fasta, ch_mirna_gtf_species ) ch_mirtop_logs = BAM_STATS_MIRNA_MIRTOP.out.stats_log ch_versions = ch_versions.mix(BAM_STATS_MIRNA_MIRTOP.out.versions) - TABLE_MERGE ( BAM_STATS_MIRNA_MIRTOP.out.counts.map{ id, tsv -> [tsv] } ) + ch_tsvs = BAM_STATS_MIRNA_MIRTOP.out.counts + .collect{it[1]} + .map{it -> return [[id:"TSVs"], it]} + + CSVTK_JOIN ( ch_tsvs ) + + TABLE_MERGE ( CSVTK_JOIN.out.csv ) ch_versions = ch_versions.mix(TABLE_MERGE.out.versions) ch_reads_genome = BOWTIE_MAP_HAIRPIN.out.unmapped diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap index 2a0e41a3..513f11be 100644 --- a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap @@ -14,7 +14,7 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_stats.txt:md5,e89c014047ffffed65f1ec4fb328e3bc" + "mirtop_stats.txt:md5,3db542a532cf3f3c8b4efda134bd6202" ] ], [ @@ -22,20 +22,20 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_stats.log:md5,49b85517828253858cc60a0390567585" + "mirtop_stats.log:md5,676d0cedfb4770f7862bc0601c2a7f15" ] ], [ - "versions.yml:md5,04fed9539a0164a116d37bf090613d42", - "versions.yml:md5,13a50e3cef16f8bb981197bbc9a46d8e", - "versions.yml:md5,5f6bea8a46cdfec82b3d8f1b6c906ac7", - "versions.yml:md5,976382d50b05cded89483e2415fde415" + "versions.yml:md5,60caed2a2383e82ed06867a75d5a50e2", + "versions.yml:md5,87d473a6cb931a2032357c3272b3249d", + "versions.yml:md5,91c635a35016586e75b620c7f33e6461", + "versions.yml:md5,b314282e0db6b00dc8acaffe182f2b80" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T23:13:48.308574263" + "timestamp": "2024-09-19T21:09:04.079276367" } } \ No newline at end of file diff --git a/tests/test_contamination_tech_reps.nf.test b/tests/test_contamination_tech_reps.nf.test index f10bccef..629c5d4a 100644 --- a/tests/test_contamination_tech_reps.nf.test +++ b/tests/test_contamination_tech_reps.nf.test @@ -5,6 +5,7 @@ nextflow_pipeline { script "main.nf" profile "test_contamination_tech_reps" tag "test_contamination_tech_reps" + tag "contamination" tag "pipeline" test("test_contamination_tech_reps") { @@ -19,7 +20,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 82 }, + { assert workflow.trace.succeeded().size() == 91 }, { assert snapshot( path("$outputDir/contaminant_filter/filter/Clone1_N1_trimmed.contamination_mqc.yaml").exists(), //TODO see if we can make these deterministic or why they are non-deterministic @@ -68,11 +69,8 @@ nextflow_pipeline { ).match("mirna_quant_edger_qc") }, { assert snapshot( - path("$outputDir/mirna_quant/mirtop/mirtop/bams_mirtop.gff").exists(), - path("$outputDir/mirna_quant/mirtop/counts/bams_mirtop.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/export/bams_mirtop_rawData.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/joined_samples_mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirna.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() ).match("mirna_quant_mirtop") }, { assert snapshot( diff --git a/tests/test_contamination_tech_reps.nf.test.snap b/tests/test_contamination_tech_reps.nf.test.snap index 84b93867..bcedfc93 100644 --- a/tests/test_contamination_tech_reps.nf.test.snap +++ b/tests/test_contamination_tech_reps.nf.test.snap @@ -34,13 +34,13 @@ }, "software_versions": { "content": [ - "{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MAP_CDNA={bowtie2=2.4.5}, MAP_NCRNA={bowtie2=2.4.5}, MAP_TRNA={bowtie2=2.4.5}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + "{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MAP_CDNA={bowtie2=2.4.5}, MAP_NCRNA={bowtie2=2.4.5}, MAP_TRNA={bowtie2=2.4.5}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T13:27:35.553235807" + "timestamp": "2024-09-20T16:43:36.482010104" }, "mirna_quant_bam": { "content": [ @@ -108,16 +108,13 @@ }, "mirna_quant_mirtop": { "content": [ - true, - true, - true, true, true ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T19:24:40.610914296" + "timestamp": "2024-09-20T18:06:26.655506797" } } \ No newline at end of file diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index e26fd984..b7ff0079 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { name "Test Workflow main.nf - test_mirgenedb" script "main.nf" profile "test_mirgenedb" - tag "test_mirgenedb" + tag "mirgenedb" tag "pipeline" test("test_mirgenedb") { diff --git a/tests/test_nextflex.nf.test b/tests/test_nextflex.nf.test index ef3c5228..4330c2b0 100644 --- a/tests/test_nextflex.nf.test +++ b/tests/test_nextflex.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { name "Test Workflow main.nf - test_nextflex" script "main.nf" profile "test_nextflex" - tag "test_nextflex" + tag "nextflex" tag "pipeline" test("test_nextflex") { @@ -19,7 +19,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 70 }, + { assert workflow.trace.succeeded().size() == 79 }, { assert snapshot( path("$outputDir/mirna_quant/bam/mature/sample2_mature.sorted.idxstats"), diff --git a/tests/test_nextflex.nf.test.snap b/tests/test_nextflex.nf.test.snap index 7148520f..393e3469 100644 --- a/tests/test_nextflex.nf.test.snap +++ b/tests/test_nextflex.nf.test.snap @@ -34,13 +34,13 @@ }, "software_versions": { "content": [ - "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T13:40:20.532779636" + "timestamp": "2024-09-20T17:11:24.272157529" }, "mirna_quant_bam": { "content": [ @@ -109,7 +109,7 @@ "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,bd72bc8bfc907c6aab72f315917ab280", "fastqc-1_sequence_duplication_levels_plot.txt:md5,a53f959bf59ad69d3bcbc53e8fe609b3", "fastqc-1_per_base_sequence_quality_plot.txt:md5,2f85a658bcb8261328449f1642688086", - "multiqc_general_stats.txt:md5,0ebd9db038faba98fd8998871a73bc23", + "multiqc_general_stats.txt:md5,9bc4353b1ae9588391be745fd069c871", "fastqc-1_per_base_n_content_plot.txt:md5,e3b4bb3ed98e87f2d8acb0c009485ecd", "fastqc-1_per_base_n_content_plot.txt:md5,e3b4bb3ed98e87f2d8acb0c009485ecd", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,2956382a3f2e855a4dce8e8246a57add", @@ -137,9 +137,9 @@ "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,ed44d5035150f69bdeb7855c80271c21" ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T03:42:09.262053409" + "timestamp": "2024-09-20T17:11:24.369706104" } } \ No newline at end of file diff --git a/tests/test_skipfastp.nf.test b/tests/test_skipfastp.nf.test index 8c29a9bf..43dfd07a 100644 --- a/tests/test_skipfastp.nf.test +++ b/tests/test_skipfastp.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { name "Test Workflow main.nf - test_skipfastp" script "main.nf" profile "test_skipfastp" - tag "test_skipfastp" + tag "skipfastp" tag "pipeline" test("test_skipfastp") { @@ -19,14 +19,11 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 58 }, + { assert workflow.trace.succeeded().size() == 63 }, { assert snapshot( - path("$outputDir/mirna_quant/mirtop/mirtop/bams_mirtop.gff").exists(), - path("$outputDir/mirna_quant/mirtop/counts/bams_mirtop.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/export/bams_mirtop_rawData.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/joined_samples_mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirna.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() ).match("mirna_quant_mirtop") }, { assert snapshot( diff --git a/tests/test_skipfastp.nf.test.snap b/tests/test_skipfastp.nf.test.snap index 098f0e35..a6fc777f 100644 --- a/tests/test_skipfastp.nf.test.snap +++ b/tests/test_skipfastp.nf.test.snap @@ -41,13 +41,13 @@ }, "software_versions": { "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T13:44:34.328354483" + "timestamp": "2024-09-20T16:48:44.385703416" }, "mirna_quant_bam": { "content": [ @@ -97,7 +97,7 @@ "multiqc_citations.txt:md5,f46d2983044658a4a89bdec5ba20fda3", "samtools-stats-dp.txt:md5,d1854b0ed73a4c9ae62a3a625c19d4b2", "fastqc_sequence_length_distribution_plot.txt:md5,ff2def0eab8321d4ed590b483641f43b", - "multiqc_general_stats.txt:md5,c548851f6cbf36dc8d0f7435b443edcd", + "multiqc_general_stats.txt:md5,3f5a47801a45a1b62bb519bea4896ab4", "fastqc_per_base_n_content_plot.txt:md5,c345fe5430e3a17ad1dbcc14e7595f50", "fastqc_per_sequence_quality_scores_plot.txt:md5,edf4d21e2928d37d94bb33a25e1d92a6", "mirtrace_qc_plot.txt:md5,49c178fc849a1aa44781ddc67c85927c", @@ -116,10 +116,10 @@ true ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T12:36:50.504361044" + "timestamp": "2024-09-20T16:48:44.52005314" }, "multiqc": { "content": [ @@ -133,16 +133,13 @@ }, "mirna_quant_mirtop": { "content": [ - true, - true, - true, true, true ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T20:38:26.512027897" + "timestamp": "2024-09-20T18:29:58.277371938" } } \ No newline at end of file diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index 1c73006e..58ef4cfa 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { name "Test Workflow main.nf - test_umi" script "main.nf" profile "test_umi" - tag "test_umi" + tag "umi" tag "pipeline" test("test_umi") { @@ -19,7 +19,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 68 }, + { assert workflow.trace.succeeded().size() == 73 }, { assert snapshot( path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), @@ -50,11 +50,8 @@ nextflow_pipeline { ).match("mirna_quant_edger_qc") }, { assert snapshot( - path("$outputDir/mirna_quant/mirtop/mirtop/bams_mirtop.gff").exists(), - path("$outputDir/mirna_quant/mirtop/counts/bams_mirtop.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/export/bams_mirtop_rawData.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/joined_samples_mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirna.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() ).match("mirna_quant_mirtop") }, { assert snapshot( diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap index 2188d7b6..5be6ed63 100644 --- a/tests/test_umi.nf.test.snap +++ b/tests/test_umi.nf.test.snap @@ -41,13 +41,13 @@ }, "software_versions": { "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T13:50:10.366114108" + "timestamp": "2024-09-20T16:55:26.495755936" }, "mirna_quant_bam": { "content": [ @@ -103,7 +103,7 @@ "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", "fastqc-1_sequence_duplication_levels_plot.txt:md5,b5ae95ecd73055798ed70947dda3747c", "fastqc-1_per_base_sequence_quality_plot.txt:md5,89adfa92b1cde0ad4e401b430bbc68ce", - "multiqc_general_stats.txt:md5,ce8b899534249cb71157e744ea0c2fd0", + "multiqc_general_stats.txt:md5,ec1bbecb2844d95f6282b893b6709a06", "fastqc-1_per_base_n_content_plot.txt:md5,db081d3aa63007e5a78113f0fc26f27d", "fastqc_per_base_n_content_plot.txt:md5,5b5b8cee3162d092c0bcddffbd000f34", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,66a47c7ce00ede2053f8e6eb20ec3417", @@ -118,10 +118,10 @@ "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", "samtools_alignment_plot.txt:md5,b5d5a2f86d2b715f310fa8d6a008123d", "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", - "mirtop_read_count_plot.txt:md5,33aaf0d8761ec2864813274f5da75943", + "mirtop_read_count_plot.txt:md5,1a250ab7f8cab415c06fbc16714a1be7", "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", - "mirtop_unique_read_count_plot.txt:md5,c1f1ea56b0a975957c3897516900df1f", - "mirtop_mean_read_count_plot.txt:md5,b2a73544ddafa79e0c39879b95b62736", + "mirtop_unique_read_count_plot.txt:md5,57463270ca5f6b5fec3f67bdf9dd1970", + "mirtop_mean_read_count_plot.txt:md5,77e38f9e8daea0f3fd2b8161d36403c5", "mirtrace_contamination_check_plot.txt:md5,2e4a51b79b8d062ff195822bfd5a91a6", "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", @@ -134,10 +134,10 @@ "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,d673e3b18c40c5af1edccffba386d678" ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-18T21:24:25.956368202" + "timestamp": "2024-09-20T16:55:26.694937898" }, "multiqc": { "content": [ @@ -151,9 +151,6 @@ }, "mirna_quant_mirtop": { "content": [ - true, - true, - true, true, true ], @@ -161,6 +158,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T21:33:55.981422488" + "timestamp": "2024-09-20T19:12:28.290360163" } } \ No newline at end of file