From e7d0f31bcceabad836566ecfcf101681242c81f5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 29 Jan 2025 16:02:35 +0000 Subject: [PATCH 1/5] Bump multiqc module --- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 ++-- modules/nf-core/multiqc/nextflow.config | 5 +++- modules/nf-core/multiqc/tests/main.nf.test | 5 ++++ .../nf-core/multiqc/tests/main.nf.test.snap | 24 +++++++++---------- 6 files changed, 25 insertions(+), 17 deletions(-) diff --git a/modules.json b/modules.json index 320f2c245..7d151208c 100644 --- a/modules.json +++ b/modules.json @@ -110,7 +110,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", "installed_by": ["modules"] }, "picard/markduplicates": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 6f5b867b7..a27122ce1 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25.1 + - bioconda::multiqc=1.27 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index cc0643e1d..58d9313c6 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:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : + 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config index ac178787c..fe5b89b2c 100644 --- a/modules/nf-core/multiqc/nextflow.config +++ b/modules/nf-core/multiqc/nextflow.config @@ -1,7 +1,10 @@ if (!params.skip_multiqc) { process { withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + ext.args = { [ + ((params.multiqc_title == null) ? '' : "--title \"${params.multiqc_title}\""), + (params.enable_multiqc_ai ? (params.multiqc_ai_type == 'full' ? '--ai-summary-full' : '--ai') : '') + ].join(' ').trim() } ext.prefix = "multiqc_report" publishDir = [ path: { [ diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f815b6de3..33316a7dd 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,11 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + + tag "modules" + tag "modules_nfcore" + tag "multiqc" + config "./nextflow.config" test("sarscov2 single-end [fastqc]") { diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2fcbb5ff7..7b7c13220 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:51:46.317523" + "timestamp": "2025-01-27T09:29:57.631982377" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:20.680978" + "timestamp": "2025-01-27T09:30:34.743726958" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:09.185842" + "timestamp": "2025-01-27T09:30:21.44383553" } } \ No newline at end of file From 20d86cba20e5b752bc34e961e18721a1bac5d110 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 29 Jan 2025 16:05:47 +0000 Subject: [PATCH 2/5] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a9c12a685..a6c6c15b4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1482](https://github.com/nf-core/rnaseq/pull/1482) - Update trimgalore module for save_unpaired fix - [PR #1486](https://github.com/nf-core/rnaseq/pull/1486) - Bump STAR build for multiprocessing fix - [PR #1490](https://github.com/nf-core/rnaseq/pull/1490) - Make genomic FASTA input optional +- [PR #1499](https://github.com/nf-core/rnaseq/pull/1499) - Bump MultiQC module to 1.27 # 3.18.0 - 2024-12-19 From 51db118de45cb754556f91946cfdbbaf77880f2d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 29 Jan 2025 16:06:12 +0000 Subject: [PATCH 3/5] Re-remove tags --- modules/nf-core/multiqc/tests/main.nf.test | 4 ---- 1 file changed, 4 deletions(-) diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7dd..cf5783238 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -4,10 +4,6 @@ nextflow_process { script "../main.nf" process "MULTIQC" - tag "modules" - tag "modules_nfcore" - tag "multiqc" - config "./nextflow.config" test("sarscov2 single-end [fastqc]") { From 613fb9e6b68299737fd5a33431b3223e8e44256c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 29 Jan 2025 16:06:48 +0000 Subject: [PATCH 4/5] Re-remove tags --- modules/nf-core/multiqc/tests/main.nf.test | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index cf5783238..f815b6de3 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" - config "./nextflow.config" test("sarscov2 single-end [fastqc]") { From 4a355a7d8cea294aa4a6baccae082f0816da5f7b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 28 Jan 2025 15:45:34 +0000 Subject: [PATCH 5/5] update snaps --- tests/default.nf.test.snap | 28 ++++++++++----------- tests/featurecounts_group_type.nf.test.snap | 26 +++++++++---------- tests/hisat2.nf.test.snap | 28 ++++++++++----------- tests/kallisto.nf.test.snap | 14 +++++------ tests/min_mapped_reads.nf.test.snap | 28 ++++++++++----------- tests/nofasta.nf.test.snap | 2 +- tests/remove_ribo_rna.nf.test.snap | 28 ++++++++++----------- tests/salmon.nf.test.snap | 14 +++++------ tests/skip_qc.nf.test.snap | 26 +++++++++---------- tests/skip_trimming.nf.test.snap | 20 +++++++-------- tests/star_rsem.nf.test.snap | 28 ++++++++++----------- tests/umi.nf.test.snap | 18 ++++++------- 12 files changed, 130 insertions(+), 130 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 6c81ba445..353b5832e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -98,10 +98,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T12:26:32.825018567" + "timestamp": "2025-01-28T13:26:07.890871152" }, "Params: default": { "content": [ @@ -367,10 +367,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1346,11 +1346,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d", + "multiqc_featurecounts_biotype_plot.txt:md5,fb9db2fca737fbdcd1a921e683805d77", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", @@ -1490,9 +1490,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T12:39:04.406597796" + "timestamp": "2025-01-28T13:24:46.099038947" } -} +} \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 8dc553d3c..8dc50d747 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -98,10 +98,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:26:42.742119846" + "timestamp": "2025-01-28T13:38:47.824968389" }, "Params: --featurecounts_group_type false": { "content": [ @@ -360,10 +360,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1313,9 +1313,9 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,d86b5743ba4486f5796327cbd2854882", "qualimap_gene_coverage_profile_Normalised.txt:md5,05618239e3183e8f312552676c4256b5", "qualimap_rnaseq_cov_hist.txt:md5,ea4b7cf07e5c7590ded5af29161db405", @@ -1440,9 +1440,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:25:47.179044158" + "timestamp": "2025-01-28T13:38:00.766111515" } -} +} \ No newline at end of file diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 6c636a54a..4669ca38d 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -99,10 +99,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:39:53.585492305" + "timestamp": "2025-01-28T13:46:14.476085587" }, "Params: --aligner hisat2": { "content": [ @@ -834,10 +834,10 @@ "multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt", "multiqc/hisat2/multiqc_report_data/multiqc_sources.txt", + "multiqc/hisat2/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/hisat2/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/hisat2/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/hisat2/multiqc_report_data/picard_deduplication.txt", - "multiqc/hisat2/multiqc_report_data/picard_histogram.txt", - "multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt", - "multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt", "multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1293,11 +1293,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e", + "multiqc_featurecounts_biotype_plot.txt:md5,6d251bec0231afccd0682e454a3b17bc", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02", "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", @@ -1340,9 +1340,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:38:50.917761241" + "timestamp": "2025-01-28T13:45:28.520702162" } -} +} \ No newline at end of file diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 3be9c4e1c..796efdfd9 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -273,10 +273,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:48:16.536464395" + "timestamp": "2025-01-28T13:49:54.341502957" }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ @@ -360,9 +360,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:49:02.306667165" + "timestamp": "2025-01-28T13:50:34.753130451" } -} +} \ No newline at end of file diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 198ebc1ae..f2f43f748 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -264,10 +264,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1077,11 +1077,11 @@ "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,d0e3792631b78e393de8e6bbbb49d476", + "multiqc_featurecounts_biotype_plot.txt:md5,7023aeba8868687d17107a265791f096", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,6d377444d29c3d4135980982ab1df2fb", "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008", "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee", @@ -1195,10 +1195,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:57:05.836924025" + "timestamp": "2025-01-28T13:58:04.624400317" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -1299,9 +1299,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T17:57:59.273391037" + "timestamp": "2025-01-28T13:58:55.550749008" } -} +} \ No newline at end of file diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap index f3593cdb6..5e9ec37d0 100644 --- a/tests/nofasta.nf.test.snap +++ b/tests/nofasta.nf.test.snap @@ -424,6 +424,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-01-21T18:27:30.970398934" + "timestamp": "2025-01-28T14:01:08.126903467" } } \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 0cb05e4df..b543e52a4 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -270,10 +270,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1262,11 +1262,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba", + "multiqc_featurecounts_biotype_plot.txt:md5,4ae746bfab7f24c39085661271ab3c57", "multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,286d47f67e1d034a88e122091ae30f3d", "qualimap_gene_coverage_profile_Normalised.txt:md5,3297068282f57506f40070b8bc6ad1b5", "qualimap_rnaseq_cov_hist.txt:md5,a523cfcb52fe8f2d5902d933568a790d", @@ -1406,10 +1406,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:13:03.469655405" + "timestamp": "2025-01-28T14:14:14.995102985" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -1513,9 +1513,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:13:56.979730403" + "timestamp": "2025-01-28T14:15:07.900489704" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index f95d31988..09d20feb7 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -349,10 +349,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T19:45:33.529844191" + "timestamp": "2025-01-28T14:18:40.084965809" }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ @@ -433,9 +433,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T19:46:22.63337267" + "timestamp": "2025-01-28T14:19:20.666237815" } -} +} \ No newline at end of file diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index ff35f4743..c2b30f4a2 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -84,10 +84,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:20:52.010478721" + "timestamp": "2025-01-28T14:26:25.392367126" }, "Params: --skip_qc": { "content": [ @@ -267,10 +267,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/salmon_plot.txt", "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt", @@ -727,9 +727,9 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", "multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,3e57c1686c863035b6e6569210dfd4a8", @@ -818,9 +818,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:20:07.800214285" + "timestamp": "2025-01-28T14:25:33.060222508" } -} +} \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 78f2d0096..15f1425d2 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -219,10 +219,10 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_salmon/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1126,11 +1126,11 @@ "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", - "multiqc_featurecounts_biotype_plot.txt:md5,91d4ea5a6d4b02091be666eeab952443", + "multiqc_featurecounts_biotype_plot.txt:md5,2fffc21e7bef2a357f5651ba64bb6cd4", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,b16bc0437cb340aaf6fa1472888b6930", "qualimap_gene_coverage_profile_Normalised.txt:md5,209b0020fcd4c3c497e3abbd1f8cd593", "qualimap_rnaseq_cov_hist.txt:md5,3be7bc41531ce84b42092a742bfeb0ab", @@ -1270,9 +1270,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:28:59.906095781" + "timestamp": "2025-01-28T14:35:13.246904514" } } \ No newline at end of file diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 31bf3c782..b2752af74 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -263,10 +263,10 @@ "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt", + "multiqc/star_rsem/multiqc_report_data/picard_MarkIlluminaAdapters_histogram.txt", + "multiqc/star_rsem/multiqc_report_data/picard_MeanQualityByCycle_histogram.txt", + "multiqc/star_rsem/multiqc_report_data/picard_QualityScoreDistribution_histogram.txt", "multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt", - "multiqc/star_rsem/multiqc_report_data/picard_histogram.txt", - "multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt", - "multiqc/star_rsem/multiqc_report_data/picard_histogram_2.txt", "multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt", "multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt", "multiqc/star_rsem/multiqc_report_data/qualimap_genomic_origin.txt", @@ -1173,11 +1173,11 @@ "multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97", - "multiqc_featurecounts_biotype_plot.txt:md5,aef45c9c7814f3127cd3e9b77a5ed676", + "multiqc_featurecounts_biotype_plot.txt:md5,16081809f893eca4d9914fd370e7fbd7", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MarkIlluminaAdapters_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_MeanQualityByCycle_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_QualityScoreDistribution_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", @@ -1290,10 +1290,10 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:37:23.242230621" + "timestamp": "2025-01-28T14:45:42.416394727" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1392,9 +1392,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.10.2" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-12-03T18:38:21.04782292" + "timestamp": "2025-01-28T14:46:52.666136139" } -} +} \ No newline at end of file diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap index b8376d44f..f7aba4613 100644 --- a/tests/umi.nf.test.snap +++ b/tests/umi.nf.test.snap @@ -1323,7 +1323,7 @@ "multiqc_cutadapt.txt:md5,0937983d3ddfeccd4ccc5b0d74477558", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a8a003b61b03295c416f3eb66c1cca65", - "multiqc_featurecounts_biotype_plot.txt:md5,5d1c33f3ff898b9bb95ed161e4235011", + "multiqc_featurecounts_biotype_plot.txt:md5,263834175c1a124e529c686b433fd005", "multiqc_samtools_idxstats.txt:md5,bdf185faa6d15d22efedb39d38c84943", "multiqc_umitools_dedup.txt:md5,bad73f567baddb2272488b0e78e208cb", "multiqc_umitools_extract.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1507,9 +1507,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2024-12-20T00:02:04.611696704" + "timestamp": "2025-01-28T15:37:17.975884153" }, "Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": { "content": [ @@ -2692,7 +2692,7 @@ "multiqc_cutadapt.txt:md5,0937983d3ddfeccd4ccc5b0d74477558", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a8a003b61b03295c416f3eb66c1cca65", - "multiqc_featurecounts_biotype_plot.txt:md5,078841c35fb163ad1e7c99393015ecac", + "multiqc_featurecounts_biotype_plot.txt:md5,aa03c08d5d2fba14d6770085bc042dbc", "multiqc_samtools_idxstats.txt:md5,35fe3b73df5ab19b53c117d3269e7e72", "qualimap_gene_coverage_profile_Counts.txt:md5,54613117acef91c2271327e31203242c", "qualimap_gene_coverage_profile_Normalised.txt:md5,f2884314cb4296877eb6ffd03a12a5b8", @@ -2745,9 +2745,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2024-12-19T22:33:42.012684597" + "timestamp": "2025-01-28T15:28:11.592812818" }, "--umi_dedup_tool 'umitools - stub": { "content": [ @@ -2858,8 +2858,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2024-12-19T23:28:01.570835895" + "timestamp": "2025-01-28T15:38:40.145569546" } -} +} \ No newline at end of file