From 24905b454e7e0c359fbc46d7dc72aca625f5538f Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 18 Sep 2024 15:29:01 +0000 Subject: [PATCH 1/7] update multiqc --- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 4 +--- modules/nf-core/multiqc/main.nf | 8 +++++--- modules/nf-core/multiqc/tests/main.nf.test | 2 ++ modules/nf-core/multiqc/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/multiqc/tests/nextflow.config | 5 +++++ 6 files changed, 18 insertions(+), 11 deletions(-) create mode 100644 modules/nf-core/multiqc/tests/nextflow.config diff --git a/modules.json b/modules.json index 5fe46b1b..1e436c29 100644 --- a/modules.json +++ b/modules.json @@ -62,7 +62,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", + "git_sha": "7c316cae26baf55e0add993bed2b0c9f7105c653", "installed_by": ["modules"] }, "samtools/flagstat": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2121492d..0fe12644 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.23 + - bioconda::multiqc=1.25 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 459dfea5..b9ccebdb 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' : - 'biocontainers/multiqc:1.23--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,9 +25,10 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ @@ -35,6 +36,7 @@ process MULTIQC { --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ $replace \\ diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 6aa27f4c..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 45e95e5d..b779e469 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -17,7 +17,7 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -29,7 +29,7 @@ "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -38,4 +38,4 @@ }, "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} From 4033ba711fbb19fadc35329345051e37f934fbda Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 18 Sep 2024 21:23:43 +0000 Subject: [PATCH 2/7] update file names --- tests/test_mirgenedb.nf.test | 20 ++++++++++---------- tests/test_nextflex.nf.test | 20 ++++++++++---------- tests/test_umi.nf.test | 20 ++++++++++---------- 3 files changed, 30 insertions(+), 30 deletions(-) diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index 5c74ab2e..78f8f613 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -81,24 +81,24 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), @@ -107,8 +107,8 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_adapter_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), diff --git a/tests/test_nextflex.nf.test b/tests/test_nextflex.nf.test index 55a5e6d5..2d276edc 100644 --- a/tests/test_nextflex.nf.test +++ b/tests/test_nextflex.nf.test @@ -94,26 +94,26 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), @@ -124,8 +124,8 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_adapter_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index 18fdd089..1c73006e 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -92,26 +92,26 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), @@ -125,8 +125,8 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_adapter_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), From e8ae2d85d628c6654cc321acc6ed581b8c6e264e Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 19 Sep 2024 04:02:21 +0000 Subject: [PATCH 3/7] update tests --- tests/test_mirgenedb.nf.test | 4 ++-- tests/test_mirgenedb.nf.test.snap | 36 ++++++++++++++-------------- tests/test_nextflex.nf.test | 6 ++--- tests/test_nextflex.nf.test.snap | 40 +++++++++++++++---------------- tests/test_umi.nf.test.snap | 40 +++++++++++++++---------------- 5 files changed, 63 insertions(+), 63 deletions(-) diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index 78f8f613..cf2244aa 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -82,7 +82,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), @@ -97,7 +97,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_overrepresented_sequences_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap index a83d2320..1222468f 100644 --- a/tests/test_mirgenedb.nf.test.snap +++ b/tests/test_mirgenedb.nf.test.snap @@ -82,46 +82,46 @@ "multiqc_multiqc_data": { "content": [ "fastqc-status-check-heatmap.txt:md5,3f897028847a4a3a5f666325cd732067", - "fastp_filtered_reads_plot.txt:md5,9159e659878ad2f538262c948f6a2345", - "fastqc_overrepresented_sequences_plot.txt:md5,2ee0e91aa9a97789b25578d0476eaf30", + "fastp_filtered_reads_plot.txt:md5,277be8c15684b9f09737bc13bcd3a055", + "fastqc_overrepresented_sequences_plot.txt:md5,7d7ecccd5d6c7fd63439785888c0c164", true, - "fastqc_sequence_counts_plot-1.txt:md5,963514191746085fcb178d3aaab0bff1", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,0a4b4285f2c53dca216c107decc9921f", + "fastqc-1_sequence_counts_plot.txt:md5,59faee895ea86c12a4124d417e3bbd63", + "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,0a4b4285f2c53dca216c107decc9921f", "multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57", "samtools-stats-dp.txt:md5,45c0315bade3f07942ded1ead37c1489", "fastqc_sequence_length_distribution_plot.txt:md5,8b5cf1e3429a1ea0b3c63cfb176e1014", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,a0502dd4f701c9deb646ffbec80c09de", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,2072cda513c8884047d9d11c8aacbf33", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,cafad80f4e07df53590cbabbbd024629", - "multiqc_general_stats.txt:md5,88f0ead7a7c0662cb580e7e40ba9d2cb", - "fastqc_per_base_n_content_plot-1.txt:md5,a0502dd4f701c9deb646ffbec80c09de", + "fastqc-1_sequence_duplication_levels_plot.txt:md5,2072cda513c8884047d9d11c8aacbf33", + "fastqc-1_per_base_sequence_quality_plot.txt:md5,cafad80f4e07df53590cbabbbd024629", + "multiqc_general_stats.txt:md5,950d3fb06c211e984084e6de9dad6bb3", + "fastqc-1_per_base_n_content_plot.txt:md5,a0502dd4f701c9deb646ffbec80c09de", "fastqc_per_base_n_content_plot.txt:md5,d907ac1ac9a4f19908b7b025eb75abfe", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,0742b9813dcc95d4c62c52c83dec390c", "fastqc_per_sequence_quality_scores_plot.txt:md5,c7aacf1ab75fbe89f86e33273aefaf26", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,6b8b8ddf52e9dcc22a4ac00c99105301", + "fastqc-1_per_sequence_quality_scores_plot.txt:md5,6b8b8ddf52e9dcc22a4ac00c99105301", true, - "fastqc_overrepresented_sequences_plot-1.txt:md5,0a2bd81443fdf55c1d2aed7fd7d73876", - "fastqc-status-check-heatmap-1.txt:md5,d9c3ce24536a948e1fe9b84c55421ab7", - "fastqc_sequence_counts_plot.txt:md5,df6cbeadce6de4c9b10f34f903efd2e1", + "fastqc-1_overrepresented_sequences_plot.txt:md5,e2e8f71f05beec9a8a7809e47ae738ad", + "fastqc-1-status-check-heatmap.txt:md5,d9c3ce24536a948e1fe9b84c55421ab7", + "fastqc_sequence_counts_plot.txt:md5,4861f0dc120e57e0359c53f417756b0c", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,e9d8e3289f84f5a1ae6775813ec5a9b4", - "samtools_alignment_plot.txt:md5,93c014a8e10d1c20589545f39f582282", + "samtools_alignment_plot.txt:md5,b841ffce110bde994ccc6e977d2f856e", "fastqc_per_base_sequence_quality_plot.txt:md5,a8adbff96d9adb317079e6becd7a80f6", "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,a0502dd4f701c9deb646ffbec80c09de", "fastqc_adapter_content_plot.txt:md5,bd0fdc9c856c55598976b5a46c23a677", "fastqc_sequence_duplication_levels_plot.txt:md5,2b1cbdce195d2aedc4bff4c5e9b618d4", "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,6906cedd750c0d43a26fdcddeacce257", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,96abe7c73fc433142fbdbacb1e67e87f", - "fastqc_adapter_content_plot-1.txt:md5,c9d77edf35d9afb8b6e86b939b5be596", + "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,96abe7c73fc433142fbdbacb1e67e87f", + "fastqc-1_adapter_content_plot.txt:md5,c9d77edf35d9afb8b6e86b939b5be596", "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,910576f4999a406ea37306b8dc4eb45b", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7cdf079a279cf080f2e2d7ab00b4f134", true, "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,585ec288b2514de54e8fb6251d1e0f98" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T20:30:51.178179907" + "timestamp": "2024-09-19T03:58:28.495279269" }, "multiqc": { "content": [ diff --git a/tests/test_nextflex.nf.test b/tests/test_nextflex.nf.test index 2d276edc..ef3c5228 100644 --- a/tests/test_nextflex.nf.test +++ b/tests/test_nextflex.nf.test @@ -93,7 +93,7 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_overrepresented_sequences_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1_top_overrepresented_sequences_table.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc-1_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), @@ -106,9 +106,9 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_base_n_content_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), diff --git a/tests/test_nextflex.nf.test.snap b/tests/test_nextflex.nf.test.snap index 52417e6b..6ae42c1a 100644 --- a/tests/test_nextflex.nf.test.snap +++ b/tests/test_nextflex.nf.test.snap @@ -97,40 +97,40 @@ "multiqc_multiqc_data": { "content": [ "fastqc-status-check-heatmap.txt:md5,949e6825a7ecc751aa9ba515de7dbd02", - "fastp_filtered_reads_plot.txt:md5,7d99da33e244ce77191b8bfeaec8180c", - "fastqc_overrepresented_sequences_plot.txt:md5,11b85c61ea97ca62a9e7c34fae9e575c", + "fastp_filtered_reads_plot.txt:md5,bf3be3a2f4b50b4de0ede0ba46336da3", + "fastqc-1_overrepresented_sequences_plot.txt:md5,11b85c61ea97ca62a9e7c34fae9e575c", true, - "fastqc_sequence_counts_plot-1.txt:md5,926304f6c18b8151a56692bb69db97e7", + "fastqc-1_sequence_counts_plot.txt:md5,0ab7661061d5e13c5493b60502921f78", "mirtrace_complexity_plot.txt:md5,127cdbec37b2ce57f6994a20796224d1", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,3f7fd27d4553da6a88f4f15dd4b6413b", + "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,3f7fd27d4553da6a88f4f15dd4b6413b", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", "samtools-stats-dp.txt:md5,1fa31e11ef6c82185d5c9dc2f40d61b2", "fastqc_sequence_length_distribution_plot.txt:md5,130a5569ba830f7e7abb971d1c8da537", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,bd72bc8bfc907c6aab72f315917ab280", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,a53f959bf59ad69d3bcbc53e8fe609b3", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,2f85a658bcb8261328449f1642688086", - "multiqc_general_stats.txt:md5,7157c8b8ac91021d1635e52d04bab58c", - "fastqc_per_base_n_content_plot-1.txt:md5,e3b4bb3ed98e87f2d8acb0c009485ecd", - "fastqc_per_base_n_content_plot.txt:md5,48710007bb055bae6f35f2fa8ea8f42b", + "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", + "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", - "fastqc_per_sequence_quality_scores_plot.txt:md5,d2339b94d6c56616b6975086bf1e23c8", - "mirtrace_qc_plot.txt:md5,98549916297e1aef4d56ef60240da14c", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,28ed13d328e755aa06a0f13f87c336eb", + "fastqc-1_per_sequence_quality_scores_plot.txt:md5,28ed13d328e755aa06a0f13f87c336eb", + "mirtrace_qc_plot.txt:md5,394ac045f75e2300302b7e3c2418cbbc", + "fastqc-1_per_sequence_quality_scores_plot.txt:md5,28ed13d328e755aa06a0f13f87c336eb", "mirtrace_length_plot.txt:md5,18717f7f295b4d03524e91fd32c2956e", true, - "fastqc-status-check-heatmap-1.txt:md5,66af5433ebb61bc68905f8219d7419ab", - "fastqc_sequence_counts_plot.txt:md5,3bfb0974e5395d2d0044586c3e4547d1", - "mirtrace_rna_categories_plot.txt:md5,b778e1bf6e9821ef770a0952d1cce164", + "fastqc-1-status-check-heatmap.txt:md5,66af5433ebb61bc68905f8219d7419ab", + "fastqc_sequence_counts_plot.txt:md5,c92bc7da83662b8a6b49d5cdbab3dc42", + "mirtrace_rna_categories_plot.txt:md5,d9f621ebb387d289357004d21c9eb209", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,e5ea2bfd87e957a18fae5239137d6499", - "samtools_alignment_plot.txt:md5,73b963380d0fc2ae145c3cd39e26824a", + "samtools_alignment_plot.txt:md5,625da9c9da2fe432bee7a5bfca9cf550", "fastqc_per_base_sequence_quality_plot.txt:md5,1208509fcaff06edcddc377c907dfdaf", "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,dd53a16aebc689109fc8065d08d8a6c7", - "mirtrace_contamination_check_plot.txt:md5,d1ba175829b82f86be8a6473b97a4676", + "mirtrace_contamination_check_plot.txt:md5,8fd040b7771963863937f0eb31a265f1", "fastqc_adapter_content_plot.txt:md5,8aa2cbcf256bbb89c4a1d1fd18019c9b", "fastqc_sequence_duplication_levels_plot.txt:md5,97a930f423f2cd365c2262b0a185f68a", "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,5857a8a1980816cf70b34b7b318e1482", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,d3ecffd88ebbdac463e297a2b98c8b3d", - "fastqc_adapter_content_plot-1.txt:md5,245d96a402988141cbe68b60a42db535", + "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,d3ecffd88ebbdac463e297a2b98c8b3d", + "fastqc-1_adapter_content_plot.txt:md5,245d96a402988141cbe68b60a42db535", "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,9033ad6887da19d96fb9e2504d8de0a5", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,fbe1f23a76ed70b2568d553fc42adef2", true, @@ -140,6 +140,6 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T22:28:11.011206343" + "timestamp": "2024-09-19T03:42:09.262053409" } } \ No newline at end of file diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap index eba77428..2ebf23c8 100644 --- a/tests/test_umi.nf.test.snap +++ b/tests/test_umi.nf.test.snap @@ -92,42 +92,42 @@ "multiqc_multiqc_data": { "content": [ "fastqc-status-check-heatmap.txt:md5,c1509fdd74b21a718fe099de64514995", - "fastp_filtered_reads_plot.txt:md5,3aaa79e1ede44347971c26100d9e954b", + "fastp_filtered_reads_plot.txt:md5,54caeafa94c6ec8de2e5fda261aee04a", true, - "fastqc_sequence_counts_plot-1.txt:md5,24744e039ce4dbcbacf42edbfd642a8b", + "fastqc-1_sequence_counts_plot.txt:md5,036a1ca02aa27567988d53bcefce1959", "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", - "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "fastqc-1_per_sequence_gc_content_plot_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", + "multiqc_citations.txt:md5,02ab194a83114a3c2c22c2749cd27717", "samtools-stats-dp.txt:md5,74808822577fb62efb39811272e6919e", "fastqc_sequence_length_distribution_plot.txt:md5,8c34b57ec084e2da9d62c254c0a517f4", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,b5ae95ecd73055798ed70947dda3747c", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,89adfa92b1cde0ad4e401b430bbc68ce", - "multiqc_general_stats.txt:md5,77248c05a5e2f0e16616603dd77dc73c", - "fastqc_per_base_n_content_plot-1.txt:md5,db081d3aa63007e5a78113f0fc26f27d", + "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", + "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", "fastqc_per_sequence_quality_scores_plot.txt:md5,3aa99649540afc898d32d2e49a364487", - "mirtrace_qc_plot.txt:md5,b08d11ea51c54e615f9608002644c787", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,4108da6fe352558a652ee2b17d609e07", + "mirtrace_qc_plot.txt:md5,98a104b1e65164016ae4081b8815f33e", + "fastqc-1_per_sequence_quality_scores_plot.txt:md5,4108da6fe352558a652ee2b17d609e07", "mirtrace_length_plot.txt:md5,440a84ce9bbdb89b736e4e2446382665", true, - "fastqc-status-check-heatmap-1.txt:md5,cb2ea844834808ae4c95c6440269cf2e", - "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", - "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", + "fastqc-1-status-check-heatmap.txt:md5,cb2ea844834808ae4c95c6440269cf2e", + "fastqc_sequence_counts_plot.txt:md5,78f80dbdcc711e490c779a998f94b69a", + "mirtrace_rna_categories_plot.txt:md5,57039a101b0062b1849dadf994df3a88", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", - "samtools_alignment_plot.txt:md5,5e828961dbd55a6d6872221c49dfdc59", + "samtools_alignment_plot.txt:md5,b5d5a2f86d2b715f310fa8d6a008123d", "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", - "mirtop_read_count_plot.txt:md5,4c8069a2123e23ece79dcc93d97f5bc4", + "mirtop_read_count_plot.txt:md5,33aaf0d8761ec2864813274f5da75943", "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", - "mirtop_unique_read_count_plot.txt:md5,12ddd823066b8218e9bf9fbac471a0b1", + "mirtop_unique_read_count_plot.txt:md5,c1f1ea56b0a975957c3897516900df1f", "mirtop_mean_read_count_plot.txt:md5,b2a73544ddafa79e0c39879b95b62736", - "mirtrace_contamination_check_plot.txt:md5,7f12917ce506127a729edb733fdda511", + "mirtrace_contamination_check_plot.txt:md5,2e4a51b79b8d062ff195822bfd5a91a6", "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c2f2f9282a50c3eef475664cc969b8ec", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,15d8fa32e0c11ef0d3d10fc28370972c", - "fastqc_adapter_content_plot-1.txt:md5,89cd342fdc6fbba5f67078c9a2f0c684", + "fastqc-1_per_sequence_gc_content_plot_Counts.txt:md5,15d8fa32e0c11ef0d3d10fc28370972c", + "fastqc-1_adapter_content_plot.txt:md5,89cd342fdc6fbba5f67078c9a2f0c684", "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f832e92fb36db181ed1079be110edb2a", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,488e25de89d18d20f29b86f2580a8df9", true, @@ -137,7 +137,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T22:21:28.306265591" + "timestamp": "2024-09-18T21:24:25.956368202" }, "multiqc": { "content": [ From 8311d40ed1e1c72a0fe7c8964fadccb439977b54 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 19 Sep 2024 12:52:46 +0000 Subject: [PATCH 4/7] update tests --- tests/test_skipfastp.nf.test.snap | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/tests/test_skipfastp.nf.test.snap b/tests/test_skipfastp.nf.test.snap index 23cee2db..79a8e03a 100644 --- a/tests/test_skipfastp.nf.test.snap +++ b/tests/test_skipfastp.nf.test.snap @@ -92,24 +92,24 @@ "multiqc_multiqc_data": { "content": [ "fastqc-status-check-heatmap.txt:md5,a16737b9ae7b9b70b0ef7e462101a729", - "fastqc_overrepresented_sequences_plot.txt:md5,0cacfefcbc37b292ae21564f845dfaa6", + "fastqc_overrepresented_sequences_plot.txt:md5,3c1ffe7d55bbf2815e6bc427a2d27a2c", "mirtrace_complexity_plot.txt:md5,e27fb1e870985b3fe76744c027ce1c40", "multiqc_citations.txt:md5,f46d2983044658a4a89bdec5ba20fda3", "samtools-stats-dp.txt:md5,d1854b0ed73a4c9ae62a3a625c19d4b2", "fastqc_sequence_length_distribution_plot.txt:md5,ff2def0eab8321d4ed590b483641f43b", - "multiqc_general_stats.txt:md5,4f9fbcd8b4395d3eb093aa242a484562", + "multiqc_general_stats.txt:md5,c548851f6cbf36dc8d0f7435b443edcd", "fastqc_per_base_n_content_plot.txt:md5,c345fe5430e3a17ad1dbcc14e7595f50", "fastqc_per_sequence_quality_scores_plot.txt:md5,edf4d21e2928d37d94bb33a25e1d92a6", - "mirtrace_qc_plot.txt:md5,75ee638eca3a02d61f2be321574488ed", + "mirtrace_qc_plot.txt:md5,49c178fc849a1aa44781ddc67c85927c", "mirtrace_length_plot.txt:md5,7023ffcd95379998adbd65204b9998ee", true, - "fastqc_sequence_counts_plot.txt:md5,da84941084250726e3828e8908640f8b", - "mirtrace_rna_categories_plot.txt:md5,6f2b9465b699df7e5c7062b6495199af", - "samtools_alignment_plot.txt:md5,2e7b7ce5aa4c69ee2b563c0376c40769", + "fastqc_sequence_counts_plot.txt:md5,a8680d3b059401e71c7c0fe2404f5933", + "mirtrace_rna_categories_plot.txt:md5,606174b789bdb9841f8e99206d147bb9", + "samtools_alignment_plot.txt:md5,2778636ce5b6c9432b67014382fc35af", "fastqc_per_base_sequence_quality_plot.txt:md5,60f539c88c503680c0b2603749494948", - "mirtop_read_count_plot.txt:md5,6820f657dc610579c53342b87fc2dcbb", - "mirtop_unique_read_count_plot.txt:md5,5015a4e2f305a707b0d2e6ddc0498eb6", - "mirtop_mean_read_count_plot.txt:md5,0148ef880eecae0c74b6a6ef2137e641", + "mirtop_read_count_plot.txt:md5,420dda9dbd3348b5c685e888dbe2a85a", + "mirtop_unique_read_count_plot.txt:md5,ade512aac4f23e63239b7db54d2544c8", + "mirtop_mean_read_count_plot.txt:md5,9f9cee399a861fd17f0627fc843b7c15", "fastqc_sequence_duplication_levels_plot.txt:md5,7e7eb4105b8f963bdf68e422e4ebce67", "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,7ac995de6a861676f64879b02d04f819", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c18bf431a08ec1230720d83781e8903b", @@ -119,7 +119,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-09-11T14:28:01.054069548" + "timestamp": "2024-09-19T12:36:50.504361044" }, "multiqc": { "content": [ From 937ae3c1eb25f953a507d81479428c367258df89 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 19 Sep 2024 14:24:27 +0000 Subject: [PATCH 5/7] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 64ca3a6d..8a6714b1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#430]](https://github.com/nf-core/smrnaseq/pull/430) - Emit a [warning if paired-end end data is used](https://github.com/nf-core/smrnaseq/issues/423) - pipeline handles SE data - [[#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`. +- [[#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. ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch From 439fdde03cf005f320be9cb900963365799561a4 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 19 Sep 2024 15:36:25 +0000 Subject: [PATCH 6/7] update modules --- conf/test_umi.config | 4 +- modules.json | 34 +- modules/nf-core/blat/environment.yml | 2 - modules/nf-core/blat/meta.yml | 2 +- modules/nf-core/blat/tests/main.nf.test | 75 ++++ modules/nf-core/blat/tests/main.nf.test.snap | 72 ++++ modules/nf-core/blat/tests/nextflow.config | 5 + modules/nf-core/cat/cat/environment.yml | 2 - modules/nf-core/cat/fastq/environment.yml | 2 - modules/nf-core/fastp/environment.yml | 2 - modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/gawk/environment.yml | 2 - .../nf-core/samtools/flagstat/environment.yml | 6 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test.snap | 16 +- .../nf-core/samtools/idxstats/environment.yml | 6 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test.snap | 16 +- .../nf-core/samtools/index/environment.yml | 6 +- modules/nf-core/samtools/index/main.nf | 4 +- .../samtools/index/tests/main.nf.test.snap | 46 +-- modules/nf-core/samtools/sort/environment.yml | 6 +- modules/nf-core/samtools/sort/main.nf | 5 +- .../samtools/sort/tests/main.nf.test.snap | 30 +- .../nf-core/samtools/stats/environment.yml | 6 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../samtools/stats/tests/main.nf.test.snap | 40 +- modules/nf-core/seqkit/grep/environment.yml | 2 - modules/nf-core/umicollapse/environment.yml | 2 - .../nf-core/umitools/extract/environment.yml | 2 - modules/nf-core/untarfiles/environment.yml | 5 +- modules/nf-core/untarfiles/main.nf | 12 +- modules/nf-core/untarfiles/tests/main.nf.test | 104 +++++ .../untarfiles/tests/main.nf.test.snap | 356 ++++++++++++++++++ .../tests/main.nf.test.snap | 80 ++-- .../tests/main.nf.test.snap | 96 ++--- .../test_contamination_tech_reps.nf.test.snap | 6 +- tests/test_mirgenedb.nf.test.snap | 28 +- tests/test_nextflex.nf.test.snap | 22 +- tests/test_skipfastp.nf.test.snap | 22 +- tests/test_umi.nf.test.snap | 26 +- 42 files changed, 882 insertions(+), 289 deletions(-) create mode 100644 modules/nf-core/blat/tests/main.nf.test create mode 100644 modules/nf-core/blat/tests/main.nf.test.snap create mode 100644 modules/nf-core/blat/tests/nextflow.config create mode 100644 modules/nf-core/untarfiles/tests/main.nf.test create mode 100644 modules/nf-core/untarfiles/tests/main.nf.test.snap diff --git a/conf/test_umi.config b/conf/test_umi.config index 16bc7256..d7dfe162 100644 --- a/conf/test_umi.config +++ b/conf/test_umi.config @@ -15,8 +15,8 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' + max_cpus = 7 + max_memory = '16.GB' max_time = '6.h' // Input data diff --git a/modules.json b/modules.json index 5053a63f..9bbf51e6 100644 --- a/modules.json +++ b/modules.json @@ -7,32 +7,32 @@ "nf-core": { "blat": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "49852039cccef84bbf5a3c0e069fac81fa3f0202", "installed_by": ["modules"] }, "cat/cat": { "branch": "master", - "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_fastp"] }, "gawk": { "branch": "master", - "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "mirtop/counts": { @@ -72,27 +72,27 @@ }, "samtools/flagstat": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/index": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["bam_stats_samtools", "modules"] }, "seqcluster/collapse": { @@ -102,23 +102,23 @@ }, "seqkit/grep": { "branch": "master", - "git_sha": "03fbf6c89e551bd8d77f3b751fb5c955f75b34c5", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"], "patch": "modules/nf-core/seqkit/grep/seqkit-grep.diff" }, "umicollapse": { "branch": "master", - "git_sha": "18e452a645bd56d1a539f53c7656e3d2915246f7", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "umitools/extract": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "untarfiles": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "958e4a6031deefa327f339f11d9baf1ab5a32d5f", "installed_by": ["modules"] } } @@ -127,7 +127,7 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["subworkflows"] }, "bam_stats_mirna_mirtop": { @@ -137,7 +137,7 @@ }, "bam_stats_samtools": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", "installed_by": ["bam_sort_stats_samtools"] }, "fastq_fastqc_umitools_fastp": { diff --git a/modules/nf-core/blat/environment.yml b/modules/nf-core/blat/environment.yml index ec2b1ff5..2a85c078 100644 --- a/modules/nf-core/blat/environment.yml +++ b/modules/nf-core/blat/environment.yml @@ -1,7 +1,5 @@ -name: blat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blat=36 diff --git a/modules/nf-core/blat/meta.yml b/modules/nf-core/blat/meta.yml index f03142d9..25deca1a 100644 --- a/modules/nf-core/blat/meta.yml +++ b/modules/nf-core/blat/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://kentinformatics.com/" documentation: "https://kentinformatics.com/documentation" doi: "10.1101/gr.229202" - licence: "['Free for academic, nonprofit and personal use']" + licence: ["Free for academic, nonprofit and personal use"] input: - meta: type: map diff --git a/modules/nf-core/blat/tests/main.nf.test b/modules/nf-core/blat/tests/main.nf.test new file mode 100644 index 00000000..8b07e5cf --- /dev/null +++ b/modules/nf-core/blat/tests/main.nf.test @@ -0,0 +1,75 @@ + +nextflow_process { + + name "Test Process BLAT" + script "../main.nf" + process "BLAT" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "blat" + tag "seqtk/seq" + + setup { + run("SEQTK_SEQ") { + script "../../seqtk/seq/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + + """ + } + } + } + + test("test-blat") { + + when { + process { + """ + input[0] = SEQTK_SEQ.out.fastx + input[1] = [ + [ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-blat-stub") { + options '-stub' + when { + process { + """ + input[0] = SEQTK_SEQ.out.fastx + input[1] = [ + [ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/blat/tests/main.nf.test.snap b/modules/nf-core/blat/tests/main.nf.test.snap new file mode 100644 index 00000000..d46a3320 --- /dev/null +++ b/modules/nf-core/blat/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-blat": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33" + ] + ], + "1": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ], + "psl": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33" + ] + ], + "versions": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T20:38:03.56409" + }, + "test-blat-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ], + "psl": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T20:38:09.736595" + } +} \ No newline at end of file diff --git a/modules/nf-core/blat/tests/nextflow.config b/modules/nf-core/blat/tests/nextflow.config new file mode 100644 index 00000000..58bc3f25 --- /dev/null +++ b/modules/nf-core/blat/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SEQTK_SEQ { + ext.args = '-A' + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index 17a04ef2..9b01c865 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -1,7 +1,5 @@ -name: cat_cat channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121..c7eb9bd1 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,7 +1,5 @@ -name: cat_fastq channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e66..26d4aca5 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,7 +1,5 @@ -name: fastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c86..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 3d98a08b..315f6dc6 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -1,7 +1,5 @@ -name: gawk channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 68b81558..09ad4c10 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,8 +1,6 @@ -name: samtools_flagstat channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 754d84b7..4a499727 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/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 23989c61..04c3852b 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 eb6c8809..09ad4c10 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,8 +1,6 @@ -name: samtools_idxstats channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 2ea2a5cc..c4b5a0a3 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/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a5ac8104..2cc89a3b 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 260d516b..09ad4c10 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,6 @@ -name: samtools_index channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b..31175610 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/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199c..72d65e81 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 36a12eab..09ad4c10 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,8 +1,6 @@ -name: samtools_sort channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099..acfd9252 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ 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) @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ 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 da38d5d1..2d6b2900 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 +149,15 @@ ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-09-16T08:50:19.061912443" }, "bam": { "content": [ @@ -167,7 +167,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" ] ], [ @@ -180,13 +180,13 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-09-16T08:49:43.971158333" } } \ 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 1cc83bd9..09ad4c10 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,8 +1,6 @@ -name: samtools_stats channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 982bc28e..493525a9 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/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 3828f378..df507be7 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/seqkit/grep/environment.yml b/modules/nf-core/seqkit/grep/environment.yml index 6f59f297..41f3e7de 100644 --- a/modules/nf-core/seqkit/grep/environment.yml +++ b/modules/nf-core/seqkit/grep/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_grep channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/umicollapse/environment.yml b/modules/nf-core/umicollapse/environment.yml index 8dbc65dc..3847980d 100644 --- a/modules/nf-core/umicollapse/environment.yml +++ b/modules/nf-core/umicollapse/environment.yml @@ -1,7 +1,5 @@ -name: umicollapse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umicollapse=1.0.0 diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index aab452d1..9f9e03c4 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -1,7 +1,5 @@ -name: umitools_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml index e479f80d..9ed33552 100644 --- a/modules/nf-core/untarfiles/environment.yml +++ b/modules/nf-core/untarfiles/environment.yml @@ -1,9 +1,8 @@ -name: untarfiles channels: - conda-forge - bioconda - - defaults + dependencies: - - conda-forge::sed=4.7 - bioconda::grep=3.4 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untarfiles/main.nf b/modules/nf-core/untarfiles/main.nf index de27e67c..bae7838c 100644 --- a/modules/nf-core/untarfiles/main.nf +++ b/modules/nf-core/untarfiles/main.nf @@ -1,11 +1,17 @@ +def deprecation_message = """ +WARNING: This module has been deprecated. + +Reason: +This module is no longer recommended for use. It is recommended to use nf-core/modules/untar +""" process UNTARFILES { tag "$archive" label 'process_single' 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' }" + 'oras://community.wave.seqera.io/library/grep_sed_tar:40b34489f8e82876' : + 'community.wave.seqera.io/library/grep_sed_tar:16f6591cd62505b3' }" input: tuple val(meta), path(archive) @@ -18,6 +24,7 @@ process UNTARFILES { task.ext.when == null || task.ext.when script: + assert true: deprecation_message def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) @@ -39,6 +46,7 @@ process UNTARFILES { """ stub: + assert true: deprecation_message prefix = task.ext.prefix ?: "${meta.id}" """ mkdir $prefix diff --git a/modules/nf-core/untarfiles/tests/main.nf.test b/modules/nf-core/untarfiles/tests/main.nf.test new file mode 100644 index 00000000..4e3acf5b --- /dev/null +++ b/modules/nf-core/untarfiles/tests/main.nf.test @@ -0,0 +1,104 @@ + +nextflow_process { + + name "Test Process UNTARFILES" + script "../main.nf" + process "UNTARFILES" + + tag "modules" + tag "modules_nfcore" + tag "untarfiles" + + test("test-untarfiles") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-untarfiles-subdirectories") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.files[0][1].collect { file(it).name }.toSorted(), + process.out.versions + ).match() + } + ) + } + } + + test("test-untarfiles-onlyfiles") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-untarfiles-onlyfiles-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/untarfiles/tests/main.nf.test.snap b/modules/nf-core/untarfiles/tests/main.nf.test.snap new file mode 100644 index 00000000..33452a08 --- /dev/null +++ b/modules/nf-core/untarfiles/tests/main.nf.test.snap @@ -0,0 +1,356 @@ +{ + "test-untarfiles-onlyfiles-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ], + "files": [ + [ + { + "id": "test" + }, + "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-29T12:22:11.239416" + }, + "test-untarfiles-subdirectories": { + "content": [ + [ + "ControlMetricsOut.bin", + "CorrectedIntMetricsOut.bin", + "ErrorMetricsOut.bin", + 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b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index b7f4da17..c3c9a049 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": 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} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap index a3ddcc5c..8ca22526 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -30,9 +30,9 @@ ] ], "3": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -62,17 +62,17 @@ ] ], "versions": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + 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"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": "2024-07-03T12:19:57.708621" + "timestamp": "2024-09-16T08:08:24.220305512" }, "test_bam_stats_samtools_paired_end_cram - stub": { "content": [ @@ -180,9 +180,9 @@ ] ], "3": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -212,17 +212,17 @@ ] ], "versions": [ - "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": "2024-07-03T12:20:17.051493" + "timestamp": "2024-09-16T08:08:54.206770141" }, "test_bam_stats_samtools_single_end": { "content": [ @@ -250,20 +250,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,4a0c429c661d6aa0b60acb9309da642d" + "test.stats:md5,291bb2393ec947140d12d42c2795b222" ] ], [ - "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": 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+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/tests/test_contamination_tech_reps.nf.test.snap b/tests/test_contamination_tech_reps.nf.test.snap index 044b7928..e7fde2d4 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=2.4.5}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, INDEX_NCRNA={bowtie2=2.4.5}, INDEX_TRNA={bowtie2=2.4.5}, 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=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, 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=2.4.5}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, INDEX_NCRNA={bowtie2=2.4.5}, INDEX_TRNA={bowtie2=2.4.5}, 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}}" ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T22:46:41.301985198" + "timestamp": "2024-09-19T14:58:18.793149636" }, "mirna_quant_bam": { "content": [ diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap index 1222468f..60cfc568 100644 --- a/tests/test_mirgenedb.nf.test.snap +++ b/tests/test_mirgenedb.nf.test.snap @@ -1,10 +1,10 @@ { "genome_quant_bam": { "content": [ - "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,26c8e55e56641f2d4387a37b099ff0c2", + "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,4fd911c09cf6e80d7914e0d77128187b", "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,aa37c5da7c2b4505ce58c3a21f97121c", - "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,03d3f6227829c80c0e29cb49df9b6a27", - "Control_N1_mature_hairpin_genome.sorted.stats:md5,6a53b78cc7e4ca2338c76095af080151", + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,eb3081fb2598ec16dd7dc369d9cefdb2", + "Control_N1_mature_hairpin_genome.sorted.stats:md5,f5b778668a95f1e4dfe2128b1168b1de", "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,5bb521c495f1c450835299b1eb88dc84", "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,6a8ad3be2ca0fa924fd32a04293d4ce4", "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,d92f9eae7657418858e6d2b69436f74f", @@ -13,19 +13,19 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T20:30:51.089034552" + "timestamp": "2024-09-19T15:14:06.322733602" }, 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"Clone9_N1_mature_hairpin.sorted.flagstat:md5,678f4f9e98c3e1fcc5af54e8dd06fbbc" ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T20:30:50.869676065" + "timestamp": "2024-09-19T15:14:06.231457002" }, "mirna_quant_edger_qc": { "content": [ diff --git a/tests/test_nextflex.nf.test.snap b/tests/test_nextflex.nf.test.snap index 6ae42c1a..d6763fee 100644 --- a/tests/test_nextflex.nf.test.snap +++ b/tests/test_nextflex.nf.test.snap @@ -34,40 +34,40 @@ }, "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=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, 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"Clone1_N3_mature.sorted.stats:md5,b1e54f83ae8a387a2071eda43ef3f9cb", true, true, true, @@ -66,9 +66,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T20:38:26.516593603" + "timestamp": "2024-09-19T15:26:42.634182624" }, "mirna_quant_edger_qc": { "content": [ diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap index 2ebf23c8..055ca66d 100644 --- a/tests/test_umi.nf.test.snap +++ b/tests/test_umi.nf.test.snap @@ -30,45 +30,45 @@ "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc", "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873", "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,c5b28a7e26947619e8c8b511a102b25f", - 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"SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats:md5,f4485713620f31d97a5006acdf6d8a5d", "SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat:md5,e0c44533bc7813d552de4864d997c916" ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T20:47:03.820560405" + "timestamp": "2024-09-19T15:35:36.685710047" }, "mirna_quant_edger_qc": { "content": [ From db440ff2d9d172e50b48bb9902b37828def150d5 Mon Sep 17 00:00:00 2001 From: atrigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 19 Sep 2024 15:54:59 +0000 Subject: [PATCH 7/7] cpus ci github --- conf/test_umi.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/test_umi.config b/conf/test_umi.config index d7dfe162..16bc7256 100644 --- a/conf/test_umi.config +++ b/conf/test_umi.config @@ -15,8 +15,8 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Limit resources so that this can run on GitHub Actions - max_cpus = 7 - max_memory = '16.GB' + max_cpus = 2 + max_memory = '6.GB' max_time = '6.h' // Input data