From 0a19f5d52163bca78341d7e8debfb1487909cfec Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Thu, 23 Jul 2026 16:29:38 +0200 Subject: [PATCH 1/8] updated phantompeakqualtools --- modules.json | 2 +- .../phantompeakqualtools/environment.yml | 1 + modules/nf-core/phantompeakqualtools/main.nf | 17 +--- modules/nf-core/phantompeakqualtools/meta.yml | 45 ++++++++-- .../phantompeakqualtools/tests/main.nf.test | 8 +- .../tests/main.nf.test.snap | 90 ++++++++++++++----- 6 files changed, 118 insertions(+), 45 deletions(-) diff --git a/modules.json b/modules.json index fa51e66f6..6a8dc6ef6 100644 --- a/modules.json +++ b/modules.json @@ -98,7 +98,7 @@ }, "phantompeakqualtools": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "git_sha": "afd8b415b67d972a6ac0d4c0a7830e3666871335", "installed_by": ["modules"] }, "picard/addorreplacereadgroups": { diff --git a/modules/nf-core/phantompeakqualtools/environment.yml b/modules/nf-core/phantompeakqualtools/environment.yml index 4eb7d8887..f6d30f0b1 100644 --- a/modules/nf-core/phantompeakqualtools/environment.yml +++ b/modules/nf-core/phantompeakqualtools/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: + - conda-forge::r-base=4.3.3 - bioconda::phantompeakqualtools=1.2.2 diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index e1f226996..a3fa409a4 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -4,7 +4,7 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4a1cddfad5b503ee347cc5de17d172e1876c547fca00aa844559c9e764fb400f/data' : 'community.wave.seqera.io/library/phantompeakqualtools:1.2.2--f8026fe2526a5e18' }" @@ -15,7 +15,8 @@ process PHANTOMPEAKQUALTOOLS { tuple val(meta), path("*.out") , emit: spp tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.Rdata"), emit: rdata - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('R'), eval('R --version | sed "1!d; s/.*version //; s/ .*//"'), topic: versions, emit: versions_r + tuple val("${task.process}"), val('phantompeakqualtools'), val('1.2.2'), topic: versions, emit: versions_phantompeakqualtools // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. when: task.ext.when == null || task.ext.when @@ -24,15 +25,10 @@ process PHANTOMPEAKQUALTOOLS { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ RUN_SPP=`which run_spp.R` Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - phantompeakqualtools: $VERSION - END_VERSIONS """ stub: @@ -42,10 +38,5 @@ process PHANTOMPEAKQUALTOOLS { touch ${prefix}.spp.pdf touch ${prefix}.spp.Rdata touch ${prefix}.spp.out - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - phantompeakqualtools: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml index 1d4eaba78..e877cc725 100644 --- a/modules/nf-core/phantompeakqualtools/meta.yml +++ b/modules/nf-core/phantompeakqualtools/meta.yml @@ -67,13 +67,46 @@ output: description: Rdata file containing the R session pattern: "*.{Rdata}" ontologies: [] + versions_r: + - - ${task.process}: + type: string + description: The name of the process + - R: + type: string + description: The name of the tool + - R --version | sed "1!d; s/.*version //; s/ .*//": + type: eval + description: The expression ot obtain the version of the tool + versions_phantompeakqualtools: + - - ${task.process}: + type: string + description: The name of the process + - phantompeakqualtools: + type: string + description: The name of the tool + - '1.2.2': + type: string + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - R: + type: string + description: The name of the tool + - R --version | sed "1!d; s/.*version //; s/ .*//": + type: eval + description: The expression ot obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - phantompeakqualtools: + type: string + description: The name of the tool + - "1.2.2": + type: string + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test b/modules/nf-core/phantompeakqualtools/tests/main.nf.test index a2eac9d3e..757a375fb 100644 --- a/modules/nf-core/phantompeakqualtools/tests/main.nf.test +++ b/modules/nf-core/phantompeakqualtools/tests/main.nf.test @@ -28,8 +28,8 @@ nextflow_process { { assert snapshot(process.out.spp, file(process.out.pdf.get(0).get(1)).name, file(process.out.rdata.get(0).get(1)).name, - process.out.versions) - .match() + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } @@ -55,8 +55,8 @@ nextflow_process { { assert snapshot(process.out.spp, file(process.out.pdf.get(0).get(1)).name, file(process.out.rdata.get(0).get(1)).name, - process.out.versions) - .match() + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap index 1021aeb8c..0885d4283 100644 --- a/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap +++ b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap @@ -30,7 +30,18 @@ ] ], "3": [ - "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" + [ + "PHANTOMPEAKQUALTOOLS", + "R", + "4.3.3" + ] + ], + "4": [ + [ + "PHANTOMPEAKQUALTOOLS", + "phantompeakqualtools", + "1.2.2" + ] ], "pdf": [ [ @@ -59,16 +70,27 @@ "test.spp.out:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" + "versions_phantompeakqualtools": [ + [ + "PHANTOMPEAKQUALTOOLS", + "phantompeakqualtools", + "1.2.2" + ] + ], + "versions_r": [ + [ + "PHANTOMPEAKQUALTOOLS", + "R", + "4.3.3" + ] ] } ], + "timestamp": "2026-07-23T12:47:39.578742", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-27T10:46:22.786363" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "sarscov2 - bam - single_end": { "content": [ @@ -83,15 +105,28 @@ ], "test.spp.pdf", "test.spp.Rdata", - [ - "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" - ] + { + "versions_phantompeakqualtools": [ + [ + "PHANTOMPEAKQUALTOOLS", + "phantompeakqualtools", + "1.2.2" + ] + ], + "versions_r": [ + [ + "PHANTOMPEAKQUALTOOLS", + "R", + "4.3.3" + ] + ] + } ], + "timestamp": "2026-07-23T12:47:30.186506", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-27T16:21:12.000709154" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "sarscov2 - bam - paired_end": { "content": [ @@ -106,14 +141,27 @@ ], "test.spp.pdf", "test.spp.Rdata", - [ - "versions.yml:md5,e0a48a40af2cf7d5de72c4c3cb47a4fc" - ] + { + "versions_phantompeakqualtools": [ + [ + "PHANTOMPEAKQUALTOOLS", + "phantompeakqualtools", + "1.2.2" + ] + ], + "versions_r": [ + [ + "PHANTOMPEAKQUALTOOLS", + "R", + "4.3.3" + ] + ] + } ], + "timestamp": "2026-07-23T12:47:35.333687", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-27T16:21:22.432426907" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file From 8c0d4c72eea8c27557154789ddebf355ce3c5944 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Thu, 23 Jul 2026 16:30:06 +0200 Subject: [PATCH 2/8] Clean up of old versions.yml --- conf/modules.config | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 087aeec16..20433d3b3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -596,8 +596,7 @@ process { ext.prefix = { "${meta.id}_peaks" } publishDir = [ path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } @@ -645,8 +644,7 @@ process { ext.prefix = { "${meta.id}.consensus_peaks" } publishDir = [ path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } From 17f88752cc554c9819ec109b9b4c75009ebf32b3 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers <57921086+Kevin-Brockers@users.noreply.github.com> Date: Thu, 23 Jul 2026 14:42:50 +0000 Subject: [PATCH 3/8] Updated Changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9b17c7311..45337952f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[PR #530](https://github.com/nf-core/chipseq/pull/530)] - Update `hommer/annotatepeaks` to topic channels. - [[#531] (https://github.com/nf-core/chipseq/issues/531)] - Changed chromap decompression - untarfiles (deprecated) to untar modules. - [[PR #533](https://github.com/nf-core/chipseq/pull/533)] - Update `khmers/uniquekmers` to topic channels. +- [[PR #534](https://github.com/nf-core/chipseq/pull/534)] - Update `phantompeakqualtools` to topic channels. ### Parameters From 501595879866894289eb518d73c11d8fc8e138df Mon Sep 17 00:00:00 2001 From: Kevin-Brockers <57921086+Kevin-Brockers@users.noreply.github.com> Date: Thu, 23 Jul 2026 20:54:41 +0000 Subject: [PATCH 4/8] updated snapshots --- tests/bowtie2.nf.test.snap | 18 +++++++++++------- tests/chromap.nf.test.snap | 20 +++++++------------- 2 files changed, 18 insertions(+), 20 deletions(-) diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap index a1a164baa..5afd04ef7 100644 --- a/tests/bowtie2.nf.test.snap +++ b/tests/bowtie2.nf.test.snap @@ -75,6 +75,10 @@ "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": { "R": "4.5.3" }, + "PHANTOMPEAKQUALTOOLS": { + "R": "4.3.3", + "phantompeakqualtools": "1.2.2" + }, "PICARD_COLLECTMULTIPLEMETRICS": { "picard": "3.4.0" }, @@ -952,20 +956,20 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], + "timestamp": "2026-07-23T15:06:33.000055512", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.1" - }, - "timestamp": "2026-07-23T13:13:17.36470343" + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } }, "bowtie2 with stub": { "content": [ 20 ], + "timestamp": "2026-07-23T15:07:14.072562255", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.0" - }, - "timestamp": "2026-07-21T12:39:15.303231" + "nextflow": "26.04.6" + } } } \ No newline at end of file diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap index 10ca51110..209cc8dda 100644 --- a/tests/chromap.nf.test.snap +++ b/tests/chromap.nf.test.snap @@ -74,6 +74,10 @@ "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": { "R": "4.5.3" }, + "PHANTOMPEAKQUALTOOLS": { + "R": "4.3.3", + "phantompeakqualtools": "1.2.2" + }, "PICARD_ADDORREPLACEREADGROUPS": { "picard": "3.4.0" }, @@ -958,20 +962,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.1" - }, - "timestamp": "2026-07-23T13:29:13.96008322" - }, - "chromap with stub": { - "content": [ - 20 - ], + "timestamp": "2026-07-23T15:22:19.603103729", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.0" - }, - "timestamp": "2026-07-21T12:50:29.057511" + "nextflow": "26.04.6" + } } } \ No newline at end of file From 9230caee9f8474b642711f5c732adda7c0983925 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Fri, 24 Jul 2026 00:14:53 +0200 Subject: [PATCH 5/8] updated remaining snapshots --- tests/default.nf.test.snap | 71 +++----------------- tests/skip_consensus_peaks.nf.test.snap | 56 +++------------- tests/skip_trimming.nf.test.snap | 19 +++--- tests/star.nf.test.snap | 87 +++---------------------- 4 files changed, 38 insertions(+), 195 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d44a6d0c6..a72acd08c 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -74,6 +74,10 @@ "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": { "R": "4.5.3" }, + "PHANTOMPEAKQUALTOOLS": { + "R": "4.3.3", + "phantompeakqualtools": "1.2.2" + }, "PICARD_COLLECTMULTIPLEMETRICS": { "picard": "3.4.0" }, @@ -520,9 +524,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -548,23 +549,11 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Counts.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Percentages.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_by_cycle.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_score_distribution.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", @@ -572,9 +561,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -598,15 +584,11 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -632,33 +614,17 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-pct.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", - "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -682,15 +648,11 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -716,33 +678,17 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Counts.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Percentages.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_by_cycle.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_score_distribution.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -766,7 +712,6 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -951,10 +896,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], + "timestamp": "2026-07-23T23:11:51.885442", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.1" - }, - "timestamp": "2026-07-23T13:48:35.7050288" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap index eb404349d..2317e6361 100644 --- a/tests/skip_consensus_peaks.nf.test.snap +++ b/tests/skip_consensus_peaks.nf.test.snap @@ -3,11 +3,11 @@ "content": [ 20 ], + "timestamp": "2026-07-23T23:30:51.610401", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" - }, - "timestamp": "2026-07-21T13:10:05.459362" + } }, "skip_consensus_peaks": { "content": [ @@ -73,6 +73,10 @@ "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": { "R": "4.5.3" }, + "PHANTOMPEAKQUALTOOLS": { + "R": "4.3.3", + "phantompeakqualtools": "1.2.2" + }, "PICARD_COLLECTMULTIPLEMETRICS": { "picard": "3.4.0" }, @@ -485,7 +489,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -509,14 +512,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", @@ -533,9 +528,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -559,13 +551,11 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -589,14 +579,6 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", @@ -605,7 +587,6 @@ "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", @@ -613,9 +594,6 @@ "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -639,13 +617,11 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -669,14 +645,6 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", @@ -693,9 +661,6 @@ "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -719,7 +684,6 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -892,10 +856,10 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], + "timestamp": "2026-07-23T23:29:39.590565", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.1" - }, - "timestamp": "2026-07-23T14:02:02.337853806" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index d01192287..d9fc6aa58 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -74,6 +74,10 @@ "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": { "R": "4.5.3" }, + "PHANTOMPEAKQUALTOOLS": { + "R": "4.3.3", + "phantompeakqualtools": "1.2.2" + }, "PICARD_COLLECTMULTIPLEMETRICS": { "picard": "3.4.0" }, @@ -498,7 +502,6 @@ "multiqc/broad_peak/multiqc_plots", "multiqc/broad_peak/multiqc_plots/pdf", "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", @@ -566,7 +569,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_adapter_content_plot.png", @@ -634,7 +636,6 @@ "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_adapter_content_plot.svg", @@ -829,20 +830,20 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], + "timestamp": "2026-07-23T23:42:33.228734", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.1" - }, - "timestamp": "2026-07-23T14:18:19.305798532" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "skip_trimming with stub": { "content": [ 190 ], + "timestamp": "2026-07-23T23:47:09.588064", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" - }, - "timestamp": "2026-07-21T13:23:05.44245" + } } } \ No newline at end of file diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap index 360d870f6..49dfbad07 100644 --- a/tests/star.nf.test.snap +++ b/tests/star.nf.test.snap @@ -67,6 +67,10 @@ "MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS": { "R": "4.5.3" }, + "PHANTOMPEAKQUALTOOLS": { + "R": "4.3.3", + "phantompeakqualtools": "1.2.2" + }, "PICARD_COLLECTMULTIPLEMETRICS": { "picard": "3.4.0" }, @@ -265,9 +269,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -293,33 +294,13 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Counts.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Percentages.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_by_cycle.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_score_distribution.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -343,15 +324,11 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -377,33 +354,13 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-pct.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", - "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", - "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", - "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", - "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", - "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -427,15 +384,11 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -461,33 +414,14 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Counts.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Percentages.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_by_cycle.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_score_distribution.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -511,7 +445,6 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -983,20 +916,20 @@ "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd" ] ], + "timestamp": "2026-07-24T00:12:11.393319", "meta": { - "nf-test": "0.9.3", - "nextflow": "26.04.1" - }, - "timestamp": "2026-07-23T14:46:30.377133073" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "star with stub": { "content": [ 20 ], + "timestamp": "2026-07-24T00:13:22.296093", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" - }, - "timestamp": "2026-07-15T12:28:44.226288" + } } } \ No newline at end of file From fe042b0dd8222d92b4bbbc85cb6f104d87064a26 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Fri, 24 Jul 2026 00:33:50 +0200 Subject: [PATCH 6/8] update snapshot --- tests/chromap.nf.test.snap | 64 +++++++------------------------------- 1 file changed, 12 insertions(+), 52 deletions(-) diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap index 209cc8dda..c9b913b91 100644 --- a/tests/chromap.nf.test.snap +++ b/tests/chromap.nf.test.snap @@ -530,9 +530,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -558,14 +555,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", @@ -573,8 +562,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Percentages.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_by_cycle.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_score_distribution.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", @@ -582,9 +569,6 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -608,15 +592,11 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", - "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", - "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -642,14 +622,6 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", @@ -657,8 +629,6 @@ "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", - "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", @@ -666,9 +636,6 @@ "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", - "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -692,15 +659,11 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", - "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", - "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -726,14 +689,6 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", @@ -742,7 +697,6 @@ "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Percentages.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_by_cycle.svg", - "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_score_distribution.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", @@ -750,9 +704,6 @@ "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", - "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -776,7 +727,6 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", - "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -962,10 +912,20 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-23T15:22:19.603103729", + "timestamp": "2026-07-24T00:32:22.074038", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nextflow": "26.04.0" + } + }, + "chromap with stub": { + "content": [ + 20 + ], + "timestamp": "2026-07-24T00:33:30.282771", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.0" } } } \ No newline at end of file From 98c6521078194f40a76098b4fea784a6adac461b Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Fri, 24 Jul 2026 10:18:22 +0200 Subject: [PATCH 7/8] updated all tests with -profile docker,emulate_amd64 --- tests/bowtie2.nf.test.snap | 8 +-- tests/chromap.nf.test.snap | 54 +++++++++++++++++- tests/default.nf.test.snap | 61 +++++++++++++++++++- tests/skip_consensus_peaks.nf.test.snap | 44 ++++++++++++++- tests/skip_trimming.nf.test.snap | 7 ++- tests/star.nf.test.snap | 75 ++++++++++++++++++++++++- 6 files changed, 236 insertions(+), 13 deletions(-) diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap index 5afd04ef7..18856daaa 100644 --- a/tests/bowtie2.nf.test.snap +++ b/tests/bowtie2.nf.test.snap @@ -956,20 +956,20 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-23T15:06:33.000055512", + "timestamp": "2026-07-24T09:13:20.719045", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nextflow": "26.04.0" } }, "bowtie2 with stub": { "content": [ 20 ], - "timestamp": "2026-07-23T15:07:14.072562255", + "timestamp": "2026-07-24T09:14:19.141863", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.6" + "nextflow": "26.04.0" } } } \ No newline at end of file diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap index c9b913b91..4177e7f0d 100644 --- a/tests/chromap.nf.test.snap +++ b/tests/chromap.nf.test.snap @@ -530,6 +530,9 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -555,6 +558,14 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", @@ -562,6 +573,8 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Percentages.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_by_cycle.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_score_distribution.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", @@ -569,6 +582,9 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -592,11 +608,15 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -622,6 +642,14 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", @@ -629,6 +657,8 @@ "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", @@ -636,6 +666,9 @@ "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", + "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -659,11 +692,15 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -689,6 +726,14 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", @@ -697,6 +742,7 @@ "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Percentages.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_by_cycle.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_score_distribution.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", @@ -704,6 +750,9 @@ "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -727,6 +776,7 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -912,7 +962,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-24T00:32:22.074038", + "timestamp": "2026-07-24T09:24:27.701718", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -922,7 +972,7 @@ "content": [ 20 ], - "timestamp": "2026-07-24T00:33:30.282771", + "timestamp": "2026-07-24T09:25:29.211272", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a72acd08c..a6f9ed8b1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -524,6 +524,9 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -549,11 +552,23 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Counts.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Percentages.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_by_cycle.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_score_distribution.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", @@ -561,6 +576,9 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -584,11 +602,15 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -614,17 +636,33 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-pct.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", + "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -648,11 +686,15 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -678,17 +720,33 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Counts.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Percentages.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_by_cycle.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_score_distribution.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -712,6 +770,7 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -896,7 +955,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-23T23:11:51.885442", + "timestamp": "2026-07-24T09:36:43.457966", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap index 2317e6361..dde2cdd3d 100644 --- a/tests/skip_consensus_peaks.nf.test.snap +++ b/tests/skip_consensus_peaks.nf.test.snap @@ -3,7 +3,7 @@ "content": [ 20 ], - "timestamp": "2026-07-23T23:30:51.610401", + "timestamp": "2026-07-24T09:48:19.518854", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -489,6 +489,7 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -512,6 +513,14 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", @@ -528,6 +537,9 @@ "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -551,11 +563,13 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -579,6 +593,14 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", @@ -587,6 +609,7 @@ "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", @@ -594,6 +617,9 @@ "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", + "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -617,11 +643,13 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -645,6 +673,14 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", @@ -661,6 +697,9 @@ "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -684,6 +723,7 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -856,7 +896,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-23T23:29:39.590565", + "timestamp": "2026-07-24T09:47:16.170912", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index d9fc6aa58..72c7cda8f 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -502,6 +502,7 @@ "multiqc/broad_peak/multiqc_plots", "multiqc/broad_peak/multiqc_plots/pdf", "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", @@ -569,6 +570,7 @@ "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc_adapter_content_plot.png", @@ -636,6 +638,7 @@ "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc_adapter_content_plot.svg", @@ -830,7 +833,7 @@ "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" ] ], - "timestamp": "2026-07-23T23:42:33.228734", + "timestamp": "2026-07-24T09:58:33.92544", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -840,7 +843,7 @@ "content": [ 190 ], - "timestamp": "2026-07-23T23:47:09.588064", + "timestamp": "2026-07-24T10:02:44.695311", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap index 49dfbad07..0b5b61196 100644 --- a/tests/star.nf.test.snap +++ b/tests/star.nf.test.snap @@ -269,6 +269,9 @@ "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_adapter_content_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", @@ -294,13 +297,33 @@ "multiqc/broad_peak/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/featureCounts_assignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/frip_score-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/nsc_coefficient-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_annotation-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/peak_count-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_readlength_plot.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Bases-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard-1_alignment_summary_Aligned_Reads-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Counts.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_insert_size_Percentages.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_by_cycle.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard-1_quality_score_distribution.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Adenine.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Cytosine.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Guanine.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Thymine.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/picard_base_distribution_by_cycle__Undetermined.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/picard_deduplication-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/read_distribution_profile.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/rsc_coefficient-pct.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.pdf", @@ -324,11 +347,15 @@ "multiqc/broad_peak/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/broad_peak/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/strand_shift_correlation.pdf", "multiqc/broad_peak/multiqc_plots/png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/broad_peak/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", + "multiqc/broad_peak/multiqc_plots/png/deeptools_fingerprint_plot.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_clustering_1.png", + "multiqc/broad_peak/multiqc_plots/png/deseq2_pca_1.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1-status-check-heatmap.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_adapter_content_plot.png", "multiqc/broad_peak/multiqc_plots/png/fastqc-1_per_base_n_content_plot.png", @@ -354,13 +381,33 @@ "multiqc/broad_peak/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/featureCounts_assignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/frip_score-pct.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/nsc_coefficient-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_annotation-pct.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/peak_count-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_readlength_plot.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Bases-pct.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard-1_alignment_summary_Aligned_Reads-pct.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Counts.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_insert_size_Percentages.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_by_cycle.png", + "multiqc/broad_peak/multiqc_plots/png/picard-1_quality_score_distribution.png", + "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Adenine.png", + "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Cytosine.png", + "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Guanine.png", + "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Thymine.png", + "multiqc/broad_peak/multiqc_plots/png/picard_base_distribution_by_cycle__Undetermined.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/broad_peak/multiqc_plots/png/picard_deduplication-pct.png", + "multiqc/broad_peak/multiqc_plots/png/read_distribution_profile.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-cnt.png", + "multiqc/broad_peak/multiqc_plots/png/rsc_coefficient-pct.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/broad_peak/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.png", @@ -384,11 +431,15 @@ "multiqc/broad_peak/multiqc_plots/png/samtools-stats-dp.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/broad_peak/multiqc_plots/png/samtools_alignment_plot-pct.png", + "multiqc/broad_peak/multiqc_plots/png/strand_shift_correlation.png", "multiqc/broad_peak/multiqc_plots/svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/broad_peak/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "multiqc/broad_peak/multiqc_plots/svg/deeptools_fingerprint_plot.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_clustering_1.svg", + "multiqc/broad_peak/multiqc_plots/svg/deseq2_pca_1.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1-status-check-heatmap.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_adapter_content_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/fastqc-1_per_base_n_content_plot.svg", @@ -414,14 +465,33 @@ "multiqc/broad_peak/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/featureCounts_assignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/frip_score-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/nsc_coefficient-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_annotation-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/peak_count-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_readlength_plot.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Bases-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard-1_alignment_summary_Aligned_Reads-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Counts.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_insert_size_Percentages.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_by_cycle.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard-1_quality_score_distribution.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Adenine.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Cytosine.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Guanine.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Thymine.svg", + "multiqc/broad_peak/multiqc_plots/svg/picard_base_distribution_by_cycle__Undetermined.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/picard_deduplication-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/read_distribution_profile.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-cnt.svg", + "multiqc/broad_peak/multiqc_plots/svg/rsc_coefficient-pct.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1-cnt.svg", @@ -445,6 +515,7 @@ "multiqc/broad_peak/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/broad_peak/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/broad_peak/multiqc_plots/svg/strand_shift_correlation.svg", "multiqc/broad_peak/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_chipseq_software_mqc_versions.yml", @@ -916,7 +987,7 @@ "SPT5_T15_REP2.mLb.clN.sorted.bam.idxstats:md5,aa2db2bcb3aa876cfbfe24b49d98aabd" ] ], - "timestamp": "2026-07-24T00:12:11.393319", + "timestamp": "2026-07-24T10:13:45.338341", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -926,7 +997,7 @@ "content": [ 20 ], - "timestamp": "2026-07-24T00:13:22.296093", + "timestamp": "2026-07-24T10:14:50.096693", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" From be0c2477e17d8b9539bb0cc70cf7972290ccce86 Mon Sep 17 00:00:00 2001 From: Kevin-Brockers Date: Fri, 24 Jul 2026 12:19:17 +0200 Subject: [PATCH 8/8] Implemented Jose's review suggestions' --- modules.json | 2 +- modules/nf-core/phantompeakqualtools/main.nf | 1 - .../nf-core/phantompeakqualtools/tests/main.nf.test.snap | 6 +++--- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/modules.json b/modules.json index 6a8dc6ef6..2d4e0e43d 100644 --- a/modules.json +++ b/modules.json @@ -98,7 +98,7 @@ }, "phantompeakqualtools": { "branch": "master", - "git_sha": "afd8b415b67d972a6ac0d4c0a7830e3666871335", + "git_sha": "003c45ac19e684cae37402d54a56e85b0e626b90", "installed_by": ["modules"] }, "picard/addorreplacereadgroups": { diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index a3fa409a4..c362dfb9d 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -33,7 +33,6 @@ process PHANTOMPEAKQUALTOOLS { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.spp.pdf touch ${prefix}.spp.Rdata diff --git a/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap index 0885d4283..18e85202c 100644 --- a/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap +++ b/modules/nf-core/phantompeakqualtools/tests/main.nf.test.snap @@ -86,7 +86,7 @@ ] } ], - "timestamp": "2026-07-23T12:47:39.578742", + "timestamp": "2026-07-24T11:59:53.747861", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -122,7 +122,7 @@ ] } ], - "timestamp": "2026-07-23T12:47:30.186506", + "timestamp": "2026-07-24T11:59:43.988452", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0" @@ -158,7 +158,7 @@ ] } ], - "timestamp": "2026-07-23T12:47:35.333687", + "timestamp": "2026-07-24T11:59:49.842671", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.0"