From 173c182350cd6c370757e35abc0ea9c78a9ceb43 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 11:29:30 +0100 Subject: [PATCH 01/10] add nanoplot to multiqc output --- conf/modules.config | 12 ++++++++---- modules/nf-core/nanoplot/main.nf | 9 +++++++++ workflows/lrsomatic.nf | 4 +++- 3 files changed, 20 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5726763c..9ffd0859 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -42,33 +42,37 @@ process { } withName: '.*:CRAMINO_PRE' { + ext.prefix = { "${meta.id}_${meta.type}" } ext.args = '--ubam' publishDir = [ path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_ubam_${meta.replicate}/" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.arrow') ? null : filename } ] } withName: '.*:CRAMINO_POST' { + ext.prefix = { "${meta.id}_${meta.type}" } publishDir = [ path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_aln" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.arrow') ? null : filename } ] } withName: '.*:NANOPLOT_PRE' { + ext.prefix = { "${meta.id}_${meta.type}_ubam" } publishDir = [ - path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}/" }, + path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam${meta.replicate}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } withName: '.*:NANOPLOT_POST' { + ext.prefix = { "${meta.id}_${meta.type}_aln" } publishDir = [ - path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" }, + path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index 2bb02b20..c87aa758 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -20,6 +20,7 @@ process NANOPLOT { task.ext.when == null || task.ext.when script: + def prefix = task.ext.prefix ?: "${meta.id}" def args = task.ext.args ?: '' def input_file = ("$ontfile".endsWith(".fastq.gz") || "$ontfile".endsWith(".fq.gz")) ? "--fastq ${ontfile}" : ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ("$ontfile".endsWith(".arrow")) ? "--arrow ${ontfile}" : '' @@ -29,6 +30,14 @@ process NANOPLOT { -t $task.cpus \\ $input_file + for nanoplot_file in *.html *.png *.txt *.log + do + if [[ -s \$nanoplot_file ]] + then + mv \$nanoplot_file ${prefix}_\$nanoplot_file + fi + done + cat <<-END_VERSIONS > versions.yml "${task.process}": nanoplot: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//') diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index aa50b0bb..80ca5b56 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -626,7 +626,7 @@ workflow LRSOMATIC { // // MODULE: MultiQC // - summary_params = paramsSummaryMap( + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( @@ -654,6 +654,8 @@ workflow LRSOMATIC { ch_multiqc_files = ch_multiqc_files.mix(ch_mosdepth_global.collect{it -> it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_mosdepth_summary.collect{it -> it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(NANOPLOT_PRE.out.txt.collect{it -> it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(NANOPLOT_POST.out.txt.collect{it -> it[1]}.ifEmpty([])) MULTIQC ( ch_multiqc_files From 47f690a54f322831fe1e025a422f825621abf833 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 11:30:31 +0100 Subject: [PATCH 02/10] prettier --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 9ffd0859..41c02385 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -72,7 +72,7 @@ process { withName: '.*:NANOPLOT_POST' { ext.prefix = { "${meta.id}_${meta.type}_aln" } publishDir = [ - path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" }, + path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] From cf9085662ef4cbfddacc0aef610c8ba07f1ad593 Mon Sep 17 00:00:00 2001 From: Luuk Harbers <40829819+ljwharbers@users.noreply.github.com> Date: Fri, 13 Mar 2026 11:39:51 +0100 Subject: [PATCH 03/10] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- modules/nf-core/nanoplot/main.nf | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf index c87aa758..ba7b9a69 100644 --- a/modules/nf-core/nanoplot/main.nf +++ b/modules/nf-core/nanoplot/main.nf @@ -45,16 +45,17 @@ process NANOPLOT { """ stub: + def prefix = task.ext.prefix ?: "${meta.id}" """ - touch LengthvsQualityScatterPlot_dot.html - touch LengthvsQualityScatterPlot_kde.html - touch NanoPlot-report.html - touch NanoStats.txt - touch Non_weightedHistogramReadlength.html - touch Non_weightedLogTransformed_HistogramReadlength.html - touch WeightedHistogramReadlength.html - touch WeightedLogTransformed_HistogramReadlength.html - touch Yield_By_Length.html + touch ${prefix}_LengthvsQualityScatterPlot_dot.html + touch ${prefix}_LengthvsQualityScatterPlot_kde.html + touch ${prefix}_NanoPlot-report.html + touch ${prefix}_NanoStats.txt + touch ${prefix}_Non_weightedHistogramReadlength.html + touch ${prefix}_Non_weightedLogTransformed_HistogramReadlength.html + touch ${prefix}_WeightedHistogramReadlength.html + touch ${prefix}_WeightedLogTransformed_HistogramReadlength.html + touch ${prefix}_Yield_By_Length.html cat <<-END_VERSIONS > versions.yml From 22fc6de893e3cd345878270ef639b619f6088748 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 11:46:42 +0100 Subject: [PATCH 04/10] snapshot, prettier and add skip_nanoplot --- nextflow.config | 1 + nextflow_schema.json | 4 + tests/default.nf.test.snap | 301 +++++++++++++++++++++---------------- workflows/lrsomatic.nf | 47 +++++- 4 files changed, 213 insertions(+), 140 deletions(-) diff --git a/nextflow.config b/nextflow.config index b03dbed8..c1315f99 100644 --- a/nextflow.config +++ b/nextflow.config @@ -32,6 +32,7 @@ params { // Skip options skip_qc = false skip_cramino = false + skip_nanoplot = false skip_mosdepth = false skip_bamstats = false skip_ascat = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 0680cc6d..b25ea2ee 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -210,6 +210,10 @@ "skip_m6a": { "type": "boolean", "description": "Skip m6a calling by Fibertools" + }, + "skip_nanoplot": { + "type": "boolean", + "description": "Skip Nanoplot" } } }, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0946f21f..8d9dba54 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -102,11 +102,13 @@ "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_nanostat.txt", "multiqc/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/multiqc_data/multiqc_samtools_idxstats.txt", "multiqc/multiqc_data/multiqc_samtools_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/nanostat_fasta_stats_table.txt", "multiqc/multiqc_data/samtools-flagstat-pct-table.txt", "multiqc/multiqc_data/samtools-flagstat-table.txt", "multiqc/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", @@ -119,6 +121,7 @@ "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-cnt.pdf", "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-pct.pdf", "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", + "multiqc/multiqc_plots/pdf/nanostat_fasta_stats_table.pdf", "multiqc/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -134,6 +137,7 @@ "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-cnt.png", "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-pct.png", "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", + "multiqc/multiqc_plots/png/nanostat_fasta_stats_table.png", "multiqc/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -149,6 +153,7 @@ "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-cnt.svg", "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-pct.svg", "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", + "multiqc/multiqc_plots/svg/nanostat_fasta_stats_table.svg", "multiqc/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -172,66 +177,62 @@ "sample1/qc", "sample1/qc/normal", "sample1/qc/normal/cramino_aln", - "sample1/qc/normal/cramino_aln/sample1.arrow", - "sample1/qc/normal/cramino_aln/sample1_cramino.txt", + "sample1/qc/normal/cramino_aln/sample1_normal_cramino.txt", "sample1/qc/normal/cramino_ubam_1", - "sample1/qc/normal/cramino_ubam_1/sample1.arrow", - "sample1/qc/normal/cramino_ubam_1/sample1_cramino.txt", + "sample1/qc/normal/cramino_ubam_1/sample1_normal_cramino.txt", "sample1/qc/normal/mosdepth", "sample1/qc/normal/mosdepth/sample1.mosdepth.global.dist.txt", "sample1/qc/normal/mosdepth/sample1.mosdepth.summary.txt", "sample1/qc/normal/nanoplot_aln", - "sample1/qc/normal/nanoplot_aln/NanoPlot-report.html", - "sample1/qc/normal/nanoplot_aln/NanoStats.txt", - "sample1/qc/normal/nanoplot_aln/Non_weightedHistogramReadlength.html", - "sample1/qc/normal/nanoplot_aln/Non_weightedLogTransformed_HistogramReadlength.html", - "sample1/qc/normal/nanoplot_aln/PercentIdentityHistogramDynamic_Histogram_percent_identity.html", - "sample1/qc/normal/nanoplot_aln/PercentIdentityvsAlignedReadLength_dot.html", - "sample1/qc/normal/nanoplot_aln/PercentIdentityvsAlignedReadLength_kde.html", - "sample1/qc/normal/nanoplot_aln/WeightedHistogramReadlength.html", - "sample1/qc/normal/nanoplot_aln/WeightedLogTransformed_HistogramReadlength.html", - "sample1/qc/normal/nanoplot_aln/Yield_By_Length.html", - "sample1/qc/normal/nanoplot_ubam_1", - "sample1/qc/normal/nanoplot_ubam_1/NanoPlot-report.html", - "sample1/qc/normal/nanoplot_ubam_1/NanoStats.txt", - "sample1/qc/normal/nanoplot_ubam_1/Non_weightedHistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam_1/Non_weightedLogTransformed_HistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam_1/WeightedHistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam_1/WeightedLogTransformed_HistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam_1/Yield_By_Length.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_NanoPlot-report.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_NanoStats.txt", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_Non_weightedHistogramReadlength.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_Non_weightedLogTransformed_HistogramReadlength.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_PercentIdentityHistogramDynamic_Histogram_percent_identity.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_PercentIdentityvsAlignedReadLength_dot.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_PercentIdentityvsAlignedReadLength_kde.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_WeightedHistogramReadlength.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_WeightedLogTransformed_HistogramReadlength.html", + "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_Yield_By_Length.html", + "sample1/qc/normal/nanoplot_ubam1", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_NanoPlot-report.html", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_NanoStats.txt", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_Non_weightedHistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_WeightedHistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_Yield_By_Length.html", "sample1/qc/normal/samtools", "sample1/qc/normal/samtools/sample1.flagstat", "sample1/qc/normal/samtools/sample1.idxstats", "sample1/qc/normal/samtools/sample1.stats", "sample1/qc/tumor", "sample1/qc/tumor/cramino_aln", - "sample1/qc/tumor/cramino_aln/sample1.arrow", - "sample1/qc/tumor/cramino_aln/sample1_cramino.txt", + "sample1/qc/tumor/cramino_aln/sample1_tumor_cramino.txt", "sample1/qc/tumor/cramino_ubam_1", - "sample1/qc/tumor/cramino_ubam_1/sample1.arrow", - "sample1/qc/tumor/cramino_ubam_1/sample1_cramino.txt", + "sample1/qc/tumor/cramino_ubam_1/sample1_tumor_cramino.txt", "sample1/qc/tumor/mosdepth", "sample1/qc/tumor/mosdepth/sample1.mosdepth.global.dist.txt", "sample1/qc/tumor/mosdepth/sample1.mosdepth.summary.txt", "sample1/qc/tumor/nanoplot_aln", - "sample1/qc/tumor/nanoplot_aln/NanoPlot-report.html", - "sample1/qc/tumor/nanoplot_aln/NanoStats.txt", - "sample1/qc/tumor/nanoplot_aln/Non_weightedHistogramReadlength.html", - "sample1/qc/tumor/nanoplot_aln/Non_weightedLogTransformed_HistogramReadlength.html", - "sample1/qc/tumor/nanoplot_aln/PercentIdentityHistogramDynamic_Histogram_percent_identity.html", - "sample1/qc/tumor/nanoplot_aln/PercentIdentityvsAlignedReadLength_dot.html", - "sample1/qc/tumor/nanoplot_aln/PercentIdentityvsAlignedReadLength_kde.html", - "sample1/qc/tumor/nanoplot_aln/WeightedHistogramReadlength.html", - "sample1/qc/tumor/nanoplot_aln/WeightedLogTransformed_HistogramReadlength.html", - "sample1/qc/tumor/nanoplot_aln/Yield_By_Length.html", - "sample1/qc/tumor/nanoplot_ubam_1", - "sample1/qc/tumor/nanoplot_ubam_1/NanoPlot-report.html", - "sample1/qc/tumor/nanoplot_ubam_1/NanoStats.txt", - "sample1/qc/tumor/nanoplot_ubam_1/Non_weightedHistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam_1/Non_weightedLogTransformed_HistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam_1/WeightedHistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam_1/WeightedLogTransformed_HistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam_1/Yield_By_Length.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_NanoPlot-report.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_NanoStats.txt", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_Non_weightedHistogramReadlength.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_Non_weightedLogTransformed_HistogramReadlength.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_PercentIdentityHistogramDynamic_Histogram_percent_identity.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_PercentIdentityvsAlignedReadLength_dot.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_PercentIdentityvsAlignedReadLength_kde.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_WeightedHistogramReadlength.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_WeightedLogTransformed_HistogramReadlength.html", + "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_Yield_By_Length.html", + "sample1/qc/tumor/nanoplot_ubam1", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_NanoPlot-report.html", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_NanoStats.txt", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_Non_weightedHistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_WeightedHistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_Yield_By_Length.html", "sample1/qc/tumor/samtools", "sample1/qc/tumor/samtools/sample1.flagstat", "sample1/qc/tumor/samtools/sample1.idxstats", @@ -245,6 +246,9 @@ "sample1/variants/clairs/indel.vcf.gz.tbi", "sample1/variants/clairs/snvs.vcf.gz", "sample1/variants/clairs/snvs.vcf.gz.tbi", + "sample1/variants/phased", + "sample1/variants/phased/somatic_smallvariants.vcf.gz", + "sample1/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample1/variants/severus", "sample1/variants/severus/all_SVs", "sample1/variants/severus/all_SVs/severus_all.vcf.gz", @@ -276,66 +280,62 @@ "sample2/qc", "sample2/qc/normal", "sample2/qc/normal/cramino_aln", - "sample2/qc/normal/cramino_aln/sample2.arrow", - "sample2/qc/normal/cramino_aln/sample2_cramino.txt", + "sample2/qc/normal/cramino_aln/sample2_normal_cramino.txt", "sample2/qc/normal/cramino_ubam_1", - "sample2/qc/normal/cramino_ubam_1/sample2.arrow", - "sample2/qc/normal/cramino_ubam_1/sample2_cramino.txt", + "sample2/qc/normal/cramino_ubam_1/sample2_normal_cramino.txt", "sample2/qc/normal/mosdepth", "sample2/qc/normal/mosdepth/sample2.mosdepth.global.dist.txt", "sample2/qc/normal/mosdepth/sample2.mosdepth.summary.txt", "sample2/qc/normal/nanoplot_aln", - "sample2/qc/normal/nanoplot_aln/NanoPlot-report.html", - "sample2/qc/normal/nanoplot_aln/NanoStats.txt", - "sample2/qc/normal/nanoplot_aln/Non_weightedHistogramReadlength.html", - "sample2/qc/normal/nanoplot_aln/Non_weightedLogTransformed_HistogramReadlength.html", - "sample2/qc/normal/nanoplot_aln/PercentIdentityHistogramDynamic_Histogram_percent_identity.html", - "sample2/qc/normal/nanoplot_aln/PercentIdentityvsAlignedReadLength_dot.html", - "sample2/qc/normal/nanoplot_aln/PercentIdentityvsAlignedReadLength_kde.html", - "sample2/qc/normal/nanoplot_aln/WeightedHistogramReadlength.html", - "sample2/qc/normal/nanoplot_aln/WeightedLogTransformed_HistogramReadlength.html", - "sample2/qc/normal/nanoplot_aln/Yield_By_Length.html", - "sample2/qc/normal/nanoplot_ubam_1", - "sample2/qc/normal/nanoplot_ubam_1/NanoPlot-report.html", - "sample2/qc/normal/nanoplot_ubam_1/NanoStats.txt", - "sample2/qc/normal/nanoplot_ubam_1/Non_weightedHistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam_1/Non_weightedLogTransformed_HistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam_1/WeightedHistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam_1/WeightedLogTransformed_HistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam_1/Yield_By_Length.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_NanoPlot-report.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_NanoStats.txt", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_Non_weightedHistogramReadlength.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_Non_weightedLogTransformed_HistogramReadlength.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_PercentIdentityHistogramDynamic_Histogram_percent_identity.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_PercentIdentityvsAlignedReadLength_dot.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_PercentIdentityvsAlignedReadLength_kde.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_WeightedHistogramReadlength.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_WeightedLogTransformed_HistogramReadlength.html", + "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_Yield_By_Length.html", + "sample2/qc/normal/nanoplot_ubam1", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_NanoPlot-report.html", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_NanoStats.txt", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_Non_weightedHistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_WeightedHistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_Yield_By_Length.html", "sample2/qc/normal/samtools", "sample2/qc/normal/samtools/sample2.flagstat", "sample2/qc/normal/samtools/sample2.idxstats", "sample2/qc/normal/samtools/sample2.stats", "sample2/qc/tumor", "sample2/qc/tumor/cramino_aln", - 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"nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2026-03-12T15:06:45.544824708" + "timestamp": "2026-03-13T11:35:37.315075475" } } \ No newline at end of file diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index 80ca5b56..fb73f922 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -156,9 +156,26 @@ workflow LRSOMATIC { downloaded_clair3_models = PREPARE_REFERENCE_FILES.out.downloaded_clair3_models + ch_nanoplot_pre_txt = channel.empty() + if (!params.skip_qc && !params.skip_cramino) { + + // + // Module: CRAMINO + // + CRAMINO_PRE( ch_samplesheet ) - NANOPLOT_PRE(CRAMINO_PRE.out.arrow) + + if (!params.skip_nanoplot) + + // + // Module: Nanoplot + // + + NANOPLOT_POST(CRAMINO_POST.out.arrow) + + } + } ch_samplesheet @@ -494,17 +511,33 @@ workflow LRSOMATIC { ) } - // - // MODULE: CRAMINO - // + + ch_nanoplot_post_txt = channel.empty() + if (!params.skip_qc && !params.skip_cramino) { + // + // MODULE: CRAMINO + // + CRAMINO_POST ( ch_minimap_bam ) - NANOPLOT_POST(CRAMINO_POST.out.arrow) + + if (!params.skip_nanoplot) + + // + // Module: Nanoplot + // + + NANOPLOT_POST(CRAMINO_POST.out.arrow) + + } + } + + // // Module: MOSDEPTH // @@ -654,8 +687,8 @@ workflow LRSOMATIC { ch_multiqc_files = ch_multiqc_files.mix(ch_mosdepth_global.collect{it -> it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_mosdepth_summary.collect{it -> it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(NANOPLOT_PRE.out.txt.collect{it -> it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(NANOPLOT_POST.out.txt.collect{it -> it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_nanoplot_pre_txt.collect{it -> it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_nanoplot_post_txt.collect{it -> it[1]}.ifEmpty([])) MULTIQC ( ch_multiqc_files From 1694671c45a3991aca1fbe1999bddde8b5b4c4c8 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 12:03:06 +0100 Subject: [PATCH 05/10] update snapshot, fix bugs --- tests/default.nf.test.snap | 77 ++++++++++++++++++-------------------- workflows/lrsomatic.nf | 6 +-- 2 files changed, 39 insertions(+), 44 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8d9dba54..3fa756e2 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -102,13 +102,11 @@ "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_nanostat.txt", "multiqc/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/multiqc_data/multiqc_samtools_idxstats.txt", "multiqc/multiqc_data/multiqc_samtools_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_data/nanostat_fasta_stats_table.txt", "multiqc/multiqc_data/samtools-flagstat-pct-table.txt", "multiqc/multiqc_data/samtools-flagstat-table.txt", "multiqc/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt", @@ -121,7 +119,6 @@ "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-cnt.pdf", "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-pct.pdf", "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", - "multiqc/multiqc_plots/pdf/nanostat_fasta_stats_table.pdf", "multiqc/multiqc_plots/pdf/samtools-flagstat-pct-table.pdf", "multiqc/multiqc_plots/pdf/samtools-flagstat-table.pdf", "multiqc/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -137,7 +134,6 @@ "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-cnt.png", "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-pct.png", "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", - "multiqc/multiqc_plots/png/nanostat_fasta_stats_table.png", "multiqc/multiqc_plots/png/samtools-flagstat-pct-table.png", "multiqc/multiqc_plots/png/samtools-flagstat-table.png", "multiqc/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -153,7 +149,6 @@ "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-cnt.svg", "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-pct.svg", "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", - "multiqc/multiqc_plots/svg/nanostat_fasta_stats_table.svg", "multiqc/multiqc_plots/svg/samtools-flagstat-pct-table.svg", "multiqc/multiqc_plots/svg/samtools-flagstat-table.svg", "multiqc/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -451,71 +446,71 @@ "sample1_normal.bam.bai:md5,398a33445ef807ebc83c851c3f3c0df6", "sample1_tumor.bam:md5,0e2ebc65d456e9aa614f5e4714ea2f97", "sample1_tumor.bam.bai:md5,b92667a80d721b8d515ad099e4f97925", - "sample1_normal_ubam_NanoPlot-report.html:md5,9b661f887209996d347c99bb6693d1fe", + "sample1_normal_ubam_NanoPlot-report.html:md5,be3693604268a0fab02485b7bb606c54", "sample1_normal_ubam_NanoStats.txt:md5,9890c05609383aa6705c684e2581493b", - 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"sample1_tumor_ubam_NanoPlot-report.html:md5,470d67e5959f233e30ce0c4e287151ea", + "sample1_tumor_ubam_NanoPlot-report.html:md5,6adc9282b33c9737d1f0b2926fe28f94", "sample1_tumor_ubam_NanoStats.txt:md5,a58520cb39ad01cf3d51d3541ae9ca34", - "sample1_tumor_ubam_Non_weightedHistogramReadlength.html:md5,d4f766699f6681bdd0a2f2b3e6fae281", - "sample1_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,56b765dfba73a5ccb1a5d4120241920d", - "sample1_tumor_ubam_WeightedHistogramReadlength.html:md5,bfc0c8b5697c66ed5426ffc17a4e749f", - "sample1_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,d505066d4c1e219545c24252ef69a856", - "sample1_tumor_ubam_Yield_By_Length.html:md5,6d1ba463e2b5bb414565776892e87002", + "sample1_tumor_ubam_Non_weightedHistogramReadlength.html:md5,9693fd625bf0abc8eb1aba5eec162a2b", + "sample1_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,39eca8028cca6776d58d9da8f30598be", + "sample1_tumor_ubam_WeightedHistogramReadlength.html:md5,edabef9208ecdac24086b2b610df233a", + "sample1_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,5a3456d2193fc25925f434931c69f329", + "sample1_tumor_ubam_Yield_By_Length.html:md5,d154845bf990aa42cb309e95200ea896", "sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample1.stats:md5,8cec99bd9c1ba4ee22619b66d4fec02a", - 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"sample2_normal_ubam_WeightedHistogramReadlength.html:md5,bb508cd4a38f2d5d3ab41cf79cd0b29f", - "sample2_normal_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,2c0dce9b1851e02d7e208f8e10c29d01", - "sample2_normal_ubam_Yield_By_Length.html:md5,7c2c0b4881e80c4a83848a1b286d9e93", + "sample2_normal_ubam_Non_weightedHistogramReadlength.html:md5,2ab39b70bb500412b20212163c3595f2", + "sample2_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,032e7db54df8901ae9e1901114b81db7", + "sample2_normal_ubam_WeightedHistogramReadlength.html:md5,7836df63068eeded963079bcc005f532", + "sample2_normal_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,948ca03bbab8ea6e2963efa25213377e", + "sample2_normal_ubam_Yield_By_Length.html:md5,edab15804d3ade11b3d5861b2e7ed363", "sample2.flagstat:md5,714d0cc0c213e2640e54a16f3d0e6e7e", "sample2.idxstats:md5,72eb83bb11748dc863fef1a0a5497e4b", "sample2.stats:md5,9afe66549bed997cce97dfa11c0f0cca", - "sample2_tumor_ubam_NanoPlot-report.html:md5,f8a2f4e4f4584caf0dfcebd4a8a95c83", + "sample2_tumor_ubam_NanoPlot-report.html:md5,23e65b98eeae335c219c03b86f0fdbe1", "sample2_tumor_ubam_NanoStats.txt:md5,0ee15432d551cfc2fc138f108c45a5f2", - 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"somatic_smallvariants.vcf.gz:md5,fd05e6540d7b8fa2ee43df2e96f812aa", - "somatic_smallvariants.vcf.gz.tbi:md5,d13967f57fe07d2289c4547a0470b1b4", + "somatic_smallvariants.vcf.gz:md5,3c4bba4e013c465ffc213e843578b8ee", + "somatic_smallvariants.vcf.gz.tbi:md5,902fd2a82e6317f9e789638efacdd613", "breakpoints_double.csv:md5,d3f0957887406fb79f9dcc3707324d8c", "read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd", "sample3_tumor.bam:md5,7107cfc84eafca8f1ae918e775111090", "sample3_tumor.bam.bai:md5,d2855691846361e01999895250c835e4", - "sample3_tumor_ubam_NanoPlot-report.html:md5,c527fd63036a768eccb2c7c7144cdf3d", + "sample3_tumor_ubam_NanoPlot-report.html:md5,07e4c71e6e82cadba4370f68bf1cccf4", "sample3_tumor_ubam_NanoStats.txt:md5,a58520cb39ad01cf3d51d3541ae9ca34", - "sample3_tumor_ubam_Non_weightedHistogramReadlength.html:md5,f474797151c3410895424ee94fedf8e8", - "sample3_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,5c465a632b11d49afe49d0682250ee96", - "sample3_tumor_ubam_WeightedHistogramReadlength.html:md5,9cbde6a54da9472708fc80af284ed4c7", - "sample3_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,76b7cbf0ae4fdf295110fe7b862db0ce", - "sample3_tumor_ubam_Yield_By_Length.html:md5,9e250d61ec770a59df33234778893305", + "sample3_tumor_ubam_Non_weightedHistogramReadlength.html:md5,66db2c981969434ca025c6fa3120fae2", + "sample3_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,2eb90ba5997c77e4bdeccbc4982c30a0", + "sample3_tumor_ubam_WeightedHistogramReadlength.html:md5,63707c0757c3eed4a779a969f8d9d9c4", + "sample3_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,e8f0ac10030973de5bf8c3b22d6414d1", + "sample3_tumor_ubam_Yield_By_Length.html:md5,fa7159e8e4e6cabc4dd64f80807412e9", "sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3.stats:md5,6825d4e497aef80ed7160afbef5076d9", - "somatic_smallvariants.vcf.gz:md5,0d47e0b09b96a9a28a5340c6866250a6", + "somatic_smallvariants.vcf.gz:md5,4e602ffaf891eb6f84daca0e178010d3", "somatic_smallvariants.vcf.gz.tbi:md5,b214ac172efbf09133bda2ab6b93987d", "breakpoints_double.csv:md5,41bb00e81dd6c319c13e754fa853ca68", "read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed" @@ -525,6 +520,6 @@ "nf-test": "0.9.2", "nextflow": "25.10.0" }, - "timestamp": "2026-03-13T11:35:37.315075475" + "timestamp": "2026-03-13T12:00:18.187202466" } } \ No newline at end of file diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index fb73f922..fc61e9c6 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -166,13 +166,13 @@ workflow LRSOMATIC { CRAMINO_PRE( ch_samplesheet ) - if (!params.skip_nanoplot) + if (!params.skip_nanoplot) { // // Module: Nanoplot // - NANOPLOT_POST(CRAMINO_POST.out.arrow) + NANOPLOT_PRE(CRAMINO_PRE.out.arrow) } @@ -523,7 +523,7 @@ workflow LRSOMATIC { CRAMINO_POST ( ch_minimap_bam ) - if (!params.skip_nanoplot) + if (!params.skip_nanoplot) { // // Module: Nanoplot From da3abafadb69431e589c362436b93f920ba3b783 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 13:25:39 +0100 Subject: [PATCH 06/10] fix snapshots --- conf/modules.config | 2 +- tests/.nftignore | 11 ++-- tests/default.nf.test.snap | 132 ++++++++++++++----------------------- 3 files changed, 56 insertions(+), 89 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 41c02385..6fad45aa 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -63,7 +63,7 @@ process { withName: '.*:NANOPLOT_PRE' { ext.prefix = { "${meta.id}_${meta.type}_ubam" } publishDir = [ - path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam${meta.replicate}" }, + path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/tests/.nftignore b/tests/.nftignore index becfbfa3..c89451e3 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -17,10 +17,7 @@ pipeline_info/*.{html,json,txt,yml} */variants/severus/read_ids.csv */variants/severus/severus.log */variants/severus/{all_SVs,somatic_SVs}/*.{vcf.gz,vcf.gz.tbi} -*/qc/{tumor,normal}/{cramino_aln}/*_cramino.txt -*/qc/{tumor,normal}/{cramino_ubam}_*/*_cramino.txt -*/qc/{tumor,normal}/{nanoplot_ubam}_*/*.html -*/qc/{tumor,normal}/{nanoplot_aln}/*.html -*/qc/{tumor,normal}/{nanoplot_ubam}_*/*.txt -*/qc/{tumor,normal}/{nanoplot_aln}/*.txt -*/qc/{tumor,normal}/{mosdepth}/*.txt +*/qc/{tumor,normal}/{cramino_ubam_,cramino_aln}/*_cramino.txt +*/qc/{tumor,normal}/{nanoplot_ubam_,nanoplot_aln}*/*.html +*/qc/{tumor,normal}/{nanoplot_ubam_,nanoplot_aln}*/*.txt +*/qc/{tumor,normal}/mosdepth/*.txt diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3fa756e2..e7bb4315 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -189,14 +189,14 @@ "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_WeightedHistogramReadlength.html", "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_WeightedLogTransformed_HistogramReadlength.html", "sample1/qc/normal/nanoplot_aln/sample1_normal_aln_Yield_By_Length.html", - "sample1/qc/normal/nanoplot_ubam1", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_NanoPlot-report.html", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_NanoStats.txt", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_Non_weightedHistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_WeightedHistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_WeightedLogTransformed_HistogramReadlength.html", - "sample1/qc/normal/nanoplot_ubam1/sample1_normal_ubam_Yield_By_Length.html", + "sample1/qc/normal/nanoplot_ubam_1", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_NanoPlot-report.html", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_NanoStats.txt", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_Non_weightedHistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_WeightedHistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample1/qc/normal/nanoplot_ubam_1/sample1_normal_ubam_Yield_By_Length.html", "sample1/qc/normal/samtools", "sample1/qc/normal/samtools/sample1.flagstat", "sample1/qc/normal/samtools/sample1.idxstats", @@ -220,14 +220,14 @@ "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_WeightedHistogramReadlength.html", "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_WeightedLogTransformed_HistogramReadlength.html", "sample1/qc/tumor/nanoplot_aln/sample1_tumor_aln_Yield_By_Length.html", - "sample1/qc/tumor/nanoplot_ubam1", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_NanoPlot-report.html", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_NanoStats.txt", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_Non_weightedHistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_WeightedHistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", - "sample1/qc/tumor/nanoplot_ubam1/sample1_tumor_ubam_Yield_By_Length.html", + "sample1/qc/tumor/nanoplot_ubam_1", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_NanoPlot-report.html", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_NanoStats.txt", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_Non_weightedHistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_WeightedHistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample1/qc/tumor/nanoplot_ubam_1/sample1_tumor_ubam_Yield_By_Length.html", "sample1/qc/tumor/samtools", "sample1/qc/tumor/samtools/sample1.flagstat", "sample1/qc/tumor/samtools/sample1.idxstats", @@ -292,14 +292,14 @@ "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_WeightedHistogramReadlength.html", "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_WeightedLogTransformed_HistogramReadlength.html", "sample2/qc/normal/nanoplot_aln/sample2_normal_aln_Yield_By_Length.html", - "sample2/qc/normal/nanoplot_ubam1", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_NanoPlot-report.html", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_NanoStats.txt", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_Non_weightedHistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_WeightedHistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_WeightedLogTransformed_HistogramReadlength.html", - "sample2/qc/normal/nanoplot_ubam1/sample2_normal_ubam_Yield_By_Length.html", + "sample2/qc/normal/nanoplot_ubam_1", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_NanoPlot-report.html", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_NanoStats.txt", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_Non_weightedHistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_WeightedHistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample2/qc/normal/nanoplot_ubam_1/sample2_normal_ubam_Yield_By_Length.html", "sample2/qc/normal/samtools", "sample2/qc/normal/samtools/sample2.flagstat", "sample2/qc/normal/samtools/sample2.idxstats", @@ -323,14 +323,14 @@ "sample2/qc/tumor/nanoplot_aln/sample2_tumor_aln_WeightedHistogramReadlength.html", "sample2/qc/tumor/nanoplot_aln/sample2_tumor_aln_WeightedLogTransformed_HistogramReadlength.html", "sample2/qc/tumor/nanoplot_aln/sample2_tumor_aln_Yield_By_Length.html", - "sample2/qc/tumor/nanoplot_ubam1", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_NanoPlot-report.html", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_NanoStats.txt", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_Non_weightedHistogramReadlength.html", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_WeightedHistogramReadlength.html", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", - "sample2/qc/tumor/nanoplot_ubam1/sample2_tumor_ubam_Yield_By_Length.html", + "sample2/qc/tumor/nanoplot_ubam_1", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_NanoPlot-report.html", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_NanoStats.txt", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_Non_weightedHistogramReadlength.html", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_WeightedHistogramReadlength.html", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample2/qc/tumor/nanoplot_ubam_1/sample2_tumor_ubam_Yield_By_Length.html", "sample2/qc/tumor/samtools", "sample2/qc/tumor/samtools/sample2.flagstat", "sample2/qc/tumor/samtools/sample2.idxstats", @@ -393,14 +393,14 @@ "sample3/qc/tumor/nanoplot_aln/sample3_tumor_aln_WeightedHistogramReadlength.html", "sample3/qc/tumor/nanoplot_aln/sample3_tumor_aln_WeightedLogTransformed_HistogramReadlength.html", "sample3/qc/tumor/nanoplot_aln/sample3_tumor_aln_Yield_By_Length.html", - "sample3/qc/tumor/nanoplot_ubam1", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_NanoPlot-report.html", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_NanoStats.txt", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_Non_weightedHistogramReadlength.html", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_WeightedHistogramReadlength.html", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", - "sample3/qc/tumor/nanoplot_ubam1/sample3_tumor_ubam_Yield_By_Length.html", + "sample3/qc/tumor/nanoplot_ubam_1", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_NanoPlot-report.html", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_NanoStats.txt", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_Non_weightedHistogramReadlength.html", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_WeightedHistogramReadlength.html", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html", + "sample3/qc/tumor/nanoplot_ubam_1/sample3_tumor_ubam_Yield_By_Length.html", "sample3/qc/tumor/samtools", "sample3/qc/tumor/samtools/sample3.flagstat", "sample3/qc/tumor/samtools/sample3.idxstats", @@ -446,72 +446,42 @@ "sample1_normal.bam.bai:md5,398a33445ef807ebc83c851c3f3c0df6", "sample1_tumor.bam:md5,0e2ebc65d456e9aa614f5e4714ea2f97", "sample1_tumor.bam.bai:md5,b92667a80d721b8d515ad099e4f97925", - "sample1_normal_ubam_NanoPlot-report.html:md5,be3693604268a0fab02485b7bb606c54", - "sample1_normal_ubam_NanoStats.txt:md5,9890c05609383aa6705c684e2581493b", - "sample1_normal_ubam_Non_weightedHistogramReadlength.html:md5,257f634cdc2a2d243508654aceb46f49", - "sample1_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,f50f7a3b17dc2ad14143a60fb6db18b6", - "sample1_normal_ubam_WeightedHistogramReadlength.html:md5,679af03ab8211478f7976849ca9aa59d", - "sample1_normal_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,fad7cc2e0a4138d5ca52fbcea013605a", - "sample1_normal_ubam_Yield_By_Length.html:md5,21cfd52990aaf1f803cb4fb56885cfcd", + "sample1_normal_cramino.txt:md5,c1d526d83fc7d5cb764b58b4fc14ec91", "sample1.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1.stats:md5,5a76f92088d36f8e93d72351e521b59b", - "sample1_tumor_ubam_NanoPlot-report.html:md5,6adc9282b33c9737d1f0b2926fe28f94", - "sample1_tumor_ubam_NanoStats.txt:md5,a58520cb39ad01cf3d51d3541ae9ca34", - "sample1_tumor_ubam_Non_weightedHistogramReadlength.html:md5,9693fd625bf0abc8eb1aba5eec162a2b", - "sample1_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,39eca8028cca6776d58d9da8f30598be", - "sample1_tumor_ubam_WeightedHistogramReadlength.html:md5,edabef9208ecdac24086b2b610df233a", - "sample1_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,5a3456d2193fc25925f434931c69f329", - "sample1_tumor_ubam_Yield_By_Length.html:md5,d154845bf990aa42cb309e95200ea896", + "sample1_tumor_cramino.txt:md5,bd89428fb05e1d1736e845b0b076fd57", "sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample1.stats:md5,8cec99bd9c1ba4ee22619b66d4fec02a", - "somatic_smallvariants.vcf.gz:md5,dcd2768bf7d67fb75025dcc0d1d0f50a", - "somatic_smallvariants.vcf.gz.tbi:md5,45ee3fde1ac766f6cb638e2aea2e3b21", + "somatic_smallvariants.vcf.gz:md5,b0f5406b7d3fd420bc2f886bc8a342ca", + "somatic_smallvariants.vcf.gz.tbi:md5,10a8341860d0d4fec1712019cad908c3", "breakpoints_double.csv:md5,fd92fe40bc0ab3b836dedc395b80d6e2", "read_qual.txt:md5,78247dfa2ea336eac0e128eba5e9eef4", "sample2_normal.bam:md5,c9b1ac8d2faec01ecb178f0b351af69c", "sample2_normal.bam.bai:md5,b8f81d2703b1d06128e23b860a9fd635", "sample2_tumor.bam:md5,2ba9456992d944b63d63e067d5e3bc56", "sample2_tumor.bam.bai:md5,8342f0fbbc8ce4f4c79aa42c7804df9d", - "sample2_normal_ubam_NanoPlot-report.html:md5,372ab1c26679e66f67f562db4f21eb2c", - "sample2_normal_ubam_NanoStats.txt:md5,11bd84cd82bf107ed257cb4c8f9438c5", - "sample2_normal_ubam_Non_weightedHistogramReadlength.html:md5,2ab39b70bb500412b20212163c3595f2", - "sample2_normal_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,032e7db54df8901ae9e1901114b81db7", - "sample2_normal_ubam_WeightedHistogramReadlength.html:md5,7836df63068eeded963079bcc005f532", - "sample2_normal_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,948ca03bbab8ea6e2963efa25213377e", - "sample2_normal_ubam_Yield_By_Length.html:md5,edab15804d3ade11b3d5861b2e7ed363", + "sample2_normal_cramino.txt:md5,445f8019e6832222c4a547fbc84a7a3f", "sample2.flagstat:md5,714d0cc0c213e2640e54a16f3d0e6e7e", "sample2.idxstats:md5,72eb83bb11748dc863fef1a0a5497e4b", "sample2.stats:md5,9afe66549bed997cce97dfa11c0f0cca", - "sample2_tumor_ubam_NanoPlot-report.html:md5,23e65b98eeae335c219c03b86f0fdbe1", - "sample2_tumor_ubam_NanoStats.txt:md5,0ee15432d551cfc2fc138f108c45a5f2", - "sample2_tumor_ubam_Non_weightedHistogramReadlength.html:md5,072094345f3e62e0b9aee109ddc110f3", - "sample2_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,143e1cfdb3ad2ad7e1e57e8b724c1114", - "sample2_tumor_ubam_WeightedHistogramReadlength.html:md5,ca1cab74c10f0150bc6cbe2c502bc83c", - "sample2_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,b7aadc77bd0009e845f76f894b888342", - "sample2_tumor_ubam_Yield_By_Length.html:md5,35711bfb1585724e1c1086b9c466e583", + "sample2_tumor_cramino.txt:md5,62eb587683ac3a32f0cc8a45dc45d466", "sample2.flagstat:md5,4344a8745efef9cc2a017024218d61c6", "sample2.idxstats:md5,69467fc02c83a30084736aeea8b785fb", "sample2.stats:md5,7cbbff1faaf2e030470a8c1e69434b48", - "somatic_smallvariants.vcf.gz:md5,3c4bba4e013c465ffc213e843578b8ee", + "somatic_smallvariants.vcf.gz:md5,d902539ee0bce31dbe91a4bcf675fb30", "somatic_smallvariants.vcf.gz.tbi:md5,902fd2a82e6317f9e789638efacdd613", "breakpoints_double.csv:md5,d3f0957887406fb79f9dcc3707324d8c", "read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd", "sample3_tumor.bam:md5,7107cfc84eafca8f1ae918e775111090", "sample3_tumor.bam.bai:md5,d2855691846361e01999895250c835e4", - "sample3_tumor_ubam_NanoPlot-report.html:md5,07e4c71e6e82cadba4370f68bf1cccf4", - "sample3_tumor_ubam_NanoStats.txt:md5,a58520cb39ad01cf3d51d3541ae9ca34", - "sample3_tumor_ubam_Non_weightedHistogramReadlength.html:md5,66db2c981969434ca025c6fa3120fae2", - "sample3_tumor_ubam_Non_weightedLogTransformed_HistogramReadlength.html:md5,2eb90ba5997c77e4bdeccbc4982c30a0", - "sample3_tumor_ubam_WeightedHistogramReadlength.html:md5,63707c0757c3eed4a779a969f8d9d9c4", - "sample3_tumor_ubam_WeightedLogTransformed_HistogramReadlength.html:md5,e8f0ac10030973de5bf8c3b22d6414d1", - "sample3_tumor_ubam_Yield_By_Length.html:md5,fa7159e8e4e6cabc4dd64f80807412e9", + "sample3_tumor_cramino.txt:md5,bd89428fb05e1d1736e845b0b076fd57", "sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3.stats:md5,6825d4e497aef80ed7160afbef5076d9", - "somatic_smallvariants.vcf.gz:md5,4e602ffaf891eb6f84daca0e178010d3", - "somatic_smallvariants.vcf.gz.tbi:md5,b214ac172efbf09133bda2ab6b93987d", + "somatic_smallvariants.vcf.gz:md5,0e556ddb228b948bcfe1eb7827e8fcf8", + "somatic_smallvariants.vcf.gz.tbi:md5,7e25c2f90223c97e94d560f0e9704854", "breakpoints_double.csv:md5,41bb00e81dd6c319c13e754fa853ca68", "read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed" ] @@ -520,6 +490,6 @@ "nf-test": "0.9.2", "nextflow": "25.10.0" }, - "timestamp": "2026-03-13T12:00:18.187202466" + "timestamp": "2026-03-13T13:20:19.591772465" } } \ No newline at end of file From a3a26556990cf0c8828bd3bfb2ba45f3995c81fd Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 13:56:47 +0100 Subject: [PATCH 07/10] fix snapshots again --- tests/.nftignore | 10 +++++++--- tests/default.nf.test.snap | 20 ++++++++++---------- 2 files changed, 17 insertions(+), 13 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index c89451e3..7a9121a9 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -17,7 +17,11 @@ pipeline_info/*.{html,json,txt,yml} */variants/severus/read_ids.csv */variants/severus/severus.log */variants/severus/{all_SVs,somatic_SVs}/*.{vcf.gz,vcf.gz.tbi} -*/qc/{tumor,normal}/{cramino_ubam_,cramino_aln}/*_cramino.txt -*/qc/{tumor,normal}/{nanoplot_ubam_,nanoplot_aln}*/*.html -*/qc/{tumor,normal}/{nanoplot_ubam_,nanoplot_aln}*/*.txt +*/variants/phased/*.{vcf.gz,vcf.gz.tbi} +*/qc/{tumor,normal}/cramino_ubam_*/*_cramino.txt +*/qc/{tumor,normal}/cramino_aln/*_cramino.txt +*/qc/{tumor,normal}/nanoplot_ubam_*/*.html +*/qc/{tumor,normal}/nanoplot_aln/*.html +*/qc/{tumor,normal}/nanoplot_ubam_*/*.txt +*/qc/{tumor,normal}/nanoplot_aln/*.txt */qc/{tumor,normal}/mosdepth/*.txt diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e7bb4315..e51766e7 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -446,15 +446,15 @@ "sample1_normal.bam.bai:md5,398a33445ef807ebc83c851c3f3c0df6", "sample1_tumor.bam:md5,0e2ebc65d456e9aa614f5e4714ea2f97", "sample1_tumor.bam.bai:md5,b92667a80d721b8d515ad099e4f97925", - "sample1_normal_cramino.txt:md5,c1d526d83fc7d5cb764b58b4fc14ec91", + "sample1_normal_cramino.txt:md5,6f9030d94213e604c4fd123726c4dc48", "sample1.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1.stats:md5,5a76f92088d36f8e93d72351e521b59b", - "sample1_tumor_cramino.txt:md5,bd89428fb05e1d1736e845b0b076fd57", + "sample1_tumor_cramino.txt:md5,d3d6eecc58eb3ddd27b0a6929051b50e", "sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample1.stats:md5,8cec99bd9c1ba4ee22619b66d4fec02a", - "somatic_smallvariants.vcf.gz:md5,b0f5406b7d3fd420bc2f886bc8a342ca", + "somatic_smallvariants.vcf.gz:md5,1ce3a6bc89598801c33f7e3433a5a468", "somatic_smallvariants.vcf.gz.tbi:md5,10a8341860d0d4fec1712019cad908c3", "breakpoints_double.csv:md5,fd92fe40bc0ab3b836dedc395b80d6e2", "read_qual.txt:md5,78247dfa2ea336eac0e128eba5e9eef4", @@ -462,26 +462,26 @@ "sample2_normal.bam.bai:md5,b8f81d2703b1d06128e23b860a9fd635", "sample2_tumor.bam:md5,2ba9456992d944b63d63e067d5e3bc56", "sample2_tumor.bam.bai:md5,8342f0fbbc8ce4f4c79aa42c7804df9d", - "sample2_normal_cramino.txt:md5,445f8019e6832222c4a547fbc84a7a3f", + "sample2_normal_cramino.txt:md5,632155c40c82c893fdaf6bb5853aab1a", "sample2.flagstat:md5,714d0cc0c213e2640e54a16f3d0e6e7e", "sample2.idxstats:md5,72eb83bb11748dc863fef1a0a5497e4b", "sample2.stats:md5,9afe66549bed997cce97dfa11c0f0cca", - "sample2_tumor_cramino.txt:md5,62eb587683ac3a32f0cc8a45dc45d466", + "sample2_tumor_cramino.txt:md5,1df7d3694566e29e3d9c46720f04cf18", "sample2.flagstat:md5,4344a8745efef9cc2a017024218d61c6", "sample2.idxstats:md5,69467fc02c83a30084736aeea8b785fb", "sample2.stats:md5,7cbbff1faaf2e030470a8c1e69434b48", - "somatic_smallvariants.vcf.gz:md5,d902539ee0bce31dbe91a4bcf675fb30", + "somatic_smallvariants.vcf.gz:md5,1eb6db5d30ea3e1ab26685deac24983d", "somatic_smallvariants.vcf.gz.tbi:md5,902fd2a82e6317f9e789638efacdd613", "breakpoints_double.csv:md5,d3f0957887406fb79f9dcc3707324d8c", "read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd", "sample3_tumor.bam:md5,7107cfc84eafca8f1ae918e775111090", "sample3_tumor.bam.bai:md5,d2855691846361e01999895250c835e4", - "sample3_tumor_cramino.txt:md5,bd89428fb05e1d1736e845b0b076fd57", + "sample3_tumor_cramino.txt:md5,d3d6eecc58eb3ddd27b0a6929051b50e", "sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3.stats:md5,6825d4e497aef80ed7160afbef5076d9", - "somatic_smallvariants.vcf.gz:md5,0e556ddb228b948bcfe1eb7827e8fcf8", - "somatic_smallvariants.vcf.gz.tbi:md5,7e25c2f90223c97e94d560f0e9704854", + "somatic_smallvariants.vcf.gz:md5,4f86dad061abc4c06481b668a2e7123f", + "somatic_smallvariants.vcf.gz.tbi:md5,b214ac172efbf09133bda2ab6b93987d", "breakpoints_double.csv:md5,41bb00e81dd6c319c13e754fa853ca68", "read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed" ] @@ -490,6 +490,6 @@ "nf-test": "0.9.2", "nextflow": "25.10.0" }, - "timestamp": "2026-03-13T13:20:19.591772465" + "timestamp": "2026-03-13T13:26:29.323724893" } } \ No newline at end of file From 9fa38036adc51a57f97fa38f544c6831af14e736 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 14:04:39 +0100 Subject: [PATCH 08/10] surely last snapshot update --- tests/default.nf.test.snap | 43 +++++++++++++++++++++++++------------- 1 file changed, 29 insertions(+), 14 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0946f21f..f0e039cd 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -245,6 +245,9 @@ "sample1/variants/clairs/indel.vcf.gz.tbi", "sample1/variants/clairs/snvs.vcf.gz", "sample1/variants/clairs/snvs.vcf.gz.tbi", + "sample1/variants/phased", + "sample1/variants/phased/somatic_smallvariants.vcf.gz", + "sample1/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample1/variants/severus", "sample1/variants/severus/all_SVs", "sample1/variants/severus/all_SVs/severus_all.vcf.gz", @@ -349,6 +352,9 @@ "sample2/variants/clairs/indel.vcf.gz.tbi", "sample2/variants/clairs/snvs.vcf.gz", "sample2/variants/clairs/snvs.vcf.gz.tbi", + "sample2/variants/phased", + "sample2/variants/phased/somatic_smallvariants.vcf.gz", + "sample2/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample2/variants/severus", "sample2/variants/severus/all_SVs", "sample2/variants/severus/all_SVs/severus_all.vcf.gz", @@ -419,6 +425,9 @@ "sample3/variants/clairsto/snv.vcf.gz.tbi", "sample3/variants/clairsto/somatic.vcf.gz", "sample3/variants/clairsto/somatic.vcf.gz.tbi", + "sample3/variants/phased", + "sample3/variants/phased/somatic_smallvariants.vcf.gz", + "sample3/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample3/variants/severus", "sample3/variants/severus/all_SVs", "sample3/variants/severus/all_SVs/severus_all.vcf.gz", @@ -443,10 +452,10 @@ "sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz_summary.html" ], [ - "sample1_normal.bam:md5,7714d4b2db4d97b609c9a58f94e9a550", - "sample1_normal.bam.bai:md5,b5e6df2994304fd78ecd2b3b8fea87ee", - "sample1_tumor.bam:md5,b0f1bdae9bbdb901eced7297088a5d1e", - "sample1_tumor.bam.bai:md5,fc1f6cd9556c7d1d08a9a52c7ee97cbb", + "sample1_normal.bam:md5,58854f8d427538288322ac20df574fe1", + "sample1_normal.bam.bai:md5,398a33445ef807ebc83c851c3f3c0df6", + "sample1_tumor.bam:md5,0e2ebc65d456e9aa614f5e4714ea2f97", + "sample1_tumor.bam.bai:md5,b92667a80d721b8d515ad099e4f97925", "sample1.arrow:md5,df57219f1bea7e7d5538ec4ee87dcf83", "sample1.arrow:md5,36467bdd847baaa060817928d30bf091", "sample1.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", @@ -457,12 +466,14 @@ "sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample1.stats:md5,8cec99bd9c1ba4ee22619b66d4fec02a", + "somatic_smallvariants.vcf.gz:md5,4b27cfd8d1c971631d464b4a0c033c9f", + "somatic_smallvariants.vcf.gz.tbi:md5,10a8341860d0d4fec1712019cad908c3", "breakpoints_double.csv:md5,fd92fe40bc0ab3b836dedc395b80d6e2", "read_qual.txt:md5,78247dfa2ea336eac0e128eba5e9eef4", - "sample2_normal.bam:md5,b2b52d2ff82220cd393fa353cf931207", - "sample2_normal.bam.bai:md5,a82a6a8a6ad1879588befe5c5869d598", - "sample2_tumor.bam:md5,f63adccc34154d53e36766ca30db1512", - "sample2_tumor.bam.bai:md5,015b8dc2ccd1e8f4338c94bc6f81ed40", + "sample2_normal.bam:md5,c9b1ac8d2faec01ecb178f0b351af69c", + "sample2_normal.bam.bai:md5,b8f81d2703b1d06128e23b860a9fd635", + "sample2_tumor.bam:md5,2ba9456992d944b63d63e067d5e3bc56", + "sample2_tumor.bam.bai:md5,8342f0fbbc8ce4f4c79aa42c7804df9d", "sample2.arrow:md5,6aa5eec1162a077f3bf8537c8f0db952", "sample2.arrow:md5,04f75058ac7edf6f8dfe33b8bab3b78d", "sample2.flagstat:md5,714d0cc0c213e2640e54a16f3d0e6e7e", @@ -473,23 +484,27 @@ "sample2.flagstat:md5,4344a8745efef9cc2a017024218d61c6", "sample2.idxstats:md5,69467fc02c83a30084736aeea8b785fb", "sample2.stats:md5,7cbbff1faaf2e030470a8c1e69434b48", + "somatic_smallvariants.vcf.gz:md5,51980a65fba01f1a611e22179a4f6692", + "somatic_smallvariants.vcf.gz.tbi:md5,a17dacb872cab6bad80c02c477118589", "breakpoints_double.csv:md5,d3f0957887406fb79f9dcc3707324d8c", "read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd", - "sample3_tumor.bam:md5,24e3b7bee7a0d8a01303f677d2b87b08", - "sample3_tumor.bam.bai:md5,d2038319977bd78352927c16ef3f1a21", + "sample3_tumor.bam:md5,7107cfc84eafca8f1ae918e775111090", + "sample3_tumor.bam.bai:md5,d2855691846361e01999895250c835e4", "sample3.arrow:md5,de5f6de5e459d71d6cd4919eea616943", "sample3.arrow:md5,b4102a193ca9eb2ebee0cd36b48c138d", "sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3.stats:md5,6825d4e497aef80ed7160afbef5076d9", + "somatic_smallvariants.vcf.gz:md5,88c02b870c57252eb964b00aacddb706", + "somatic_smallvariants.vcf.gz.tbi:md5,29931b98ac1eb3e63a01f9eada1c789b", "breakpoints_double.csv:md5,41bb00e81dd6c319c13e754fa853ca68", "read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed" ] ], + "timestamp": "2026-03-13T14:01:29.660410344", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-12T15:06:45.544824708" + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } } } \ No newline at end of file From d9a084ed75995c2e8687227a6909746baa131d67 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 14:18:45 +0100 Subject: [PATCH 09/10] surely last one --- tests/default.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f0e039cd..0fcb7191 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -466,7 +466,7 @@ "sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample1.stats:md5,8cec99bd9c1ba4ee22619b66d4fec02a", - "somatic_smallvariants.vcf.gz:md5,4b27cfd8d1c971631d464b4a0c033c9f", + "somatic_smallvariants.vcf.gz:md5,600a03c95044fcfe393d1b28cd2da843", "somatic_smallvariants.vcf.gz.tbi:md5,10a8341860d0d4fec1712019cad908c3", "breakpoints_double.csv:md5,fd92fe40bc0ab3b836dedc395b80d6e2", "read_qual.txt:md5,78247dfa2ea336eac0e128eba5e9eef4", @@ -484,8 +484,8 @@ "sample2.flagstat:md5,4344a8745efef9cc2a017024218d61c6", "sample2.idxstats:md5,69467fc02c83a30084736aeea8b785fb", "sample2.stats:md5,7cbbff1faaf2e030470a8c1e69434b48", - "somatic_smallvariants.vcf.gz:md5,51980a65fba01f1a611e22179a4f6692", - "somatic_smallvariants.vcf.gz.tbi:md5,a17dacb872cab6bad80c02c477118589", + "somatic_smallvariants.vcf.gz:md5,e4f97ca54d31c5d4ad7825000bbed360", + "somatic_smallvariants.vcf.gz.tbi:md5,d13967f57fe07d2289c4547a0470b1b4", "breakpoints_double.csv:md5,d3f0957887406fb79f9dcc3707324d8c", "read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd", "sample3_tumor.bam:md5,7107cfc84eafca8f1ae918e775111090", @@ -495,13 +495,13 @@ "sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3.stats:md5,6825d4e497aef80ed7160afbef5076d9", - "somatic_smallvariants.vcf.gz:md5,88c02b870c57252eb964b00aacddb706", - "somatic_smallvariants.vcf.gz.tbi:md5,29931b98ac1eb3e63a01f9eada1c789b", + "somatic_smallvariants.vcf.gz:md5,aab6f707ba2d3692ca3baf7cfb3e1e50", + "somatic_smallvariants.vcf.gz.tbi:md5,8c7f724be3d927cce507f15fa0f3f45d", "breakpoints_double.csv:md5,41bb00e81dd6c319c13e754fa853ca68", "read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed" ] ], - "timestamp": "2026-03-13T14:01:29.660410344", + "timestamp": "2026-03-13T14:09:46.004582221", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.0" From 943533a290a57ad82e630a4264498004e93fe689 Mon Sep 17 00:00:00 2001 From: ljwharbers Date: Fri, 13 Mar 2026 14:29:08 +0100 Subject: [PATCH 10/10] surely last time --- tests/default.nf.test.snap | 34 ++++++++++++++++------------------ 1 file changed, 16 insertions(+), 18 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 68600f89..bd36bc15 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -241,6 +241,9 @@ "sample1/variants/clairs/indel.vcf.gz.tbi", "sample1/variants/clairs/snvs.vcf.gz", "sample1/variants/clairs/snvs.vcf.gz.tbi", + "sample1/variants/phased", + "sample1/variants/phased/somatic_smallvariants.vcf.gz", + "sample1/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample1/variants/severus", "sample1/variants/severus/all_SVs", "sample1/variants/severus/all_SVs/severus_all.vcf.gz", @@ -341,6 +344,9 @@ "sample2/variants/clairs/indel.vcf.gz.tbi", "sample2/variants/clairs/snvs.vcf.gz", "sample2/variants/clairs/snvs.vcf.gz.tbi", + "sample2/variants/phased", + "sample2/variants/phased/somatic_smallvariants.vcf.gz", + "sample2/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample2/variants/severus", "sample2/variants/severus/all_SVs", "sample2/variants/severus/all_SVs/severus_all.vcf.gz", @@ -409,6 +415,9 @@ "sample3/variants/clairsto/snv.vcf.gz.tbi", "sample3/variants/clairsto/somatic.vcf.gz", "sample3/variants/clairsto/somatic.vcf.gz.tbi", + "sample3/variants/phased", + "sample3/variants/phased/somatic_smallvariants.vcf.gz", + "sample3/variants/phased/somatic_smallvariants.vcf.gz.tbi", "sample3/variants/severus", "sample3/variants/severus/all_SVs", "sample3/variants/severus/all_SVs/severus_all.vcf.gz", @@ -437,50 +446,39 @@ "sample1_normal.bam.bai:md5,398a33445ef807ebc83c851c3f3c0df6", "sample1_tumor.bam:md5,0e2ebc65d456e9aa614f5e4714ea2f97", "sample1_tumor.bam.bai:md5,b92667a80d721b8d515ad099e4f97925", - "sample1_normal_cramino.txt:md5,6f9030d94213e604c4fd123726c4dc48", "sample1.flagstat:md5,1c41ea9923945501eb7e41f83a90502d", "sample1.idxstats:md5,902e503387799123ea59255e3fca172c", "sample1.stats:md5,5a76f92088d36f8e93d72351e521b59b", - "sample1_tumor_cramino.txt:md5,d3d6eecc58eb3ddd27b0a6929051b50e", "sample1.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample1.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample1.stats:md5,8cec99bd9c1ba4ee22619b66d4fec02a", "breakpoints_double.csv:md5,fd92fe40bc0ab3b836dedc395b80d6e2", "read_qual.txt:md5,78247dfa2ea336eac0e128eba5e9eef4", - "sample2_normal.bam:md5,b2b52d2ff82220cd393fa353cf931207", - "sample2_normal.bam.bai:md5,a82a6a8a6ad1879588befe5c5869d598", - "sample2_tumor.bam:md5,f63adccc34154d53e36766ca30db1512", - "sample2_tumor.bam.bai:md5,015b8dc2ccd1e8f4338c94bc6f81ed40", - "sample2.arrow:md5,6aa5eec1162a077f3bf8537c8f0db952", - "sample2.arrow:md5,04f75058ac7edf6f8dfe33b8bab3b78d", + "sample2_normal.bam:md5,c9b1ac8d2faec01ecb178f0b351af69c", + "sample2_normal.bam.bai:md5,b8f81d2703b1d06128e23b860a9fd635", + "sample2_tumor.bam:md5,2ba9456992d944b63d63e067d5e3bc56", + "sample2_tumor.bam.bai:md5,8342f0fbbc8ce4f4c79aa42c7804df9d", "sample2.flagstat:md5,714d0cc0c213e2640e54a16f3d0e6e7e", "sample2.idxstats:md5,72eb83bb11748dc863fef1a0a5497e4b", "sample2.stats:md5,9afe66549bed997cce97dfa11c0f0cca", - "sample2_tumor_cramino.txt:md5,1df7d3694566e29e3d9c46720f04cf18", "sample2.flagstat:md5,4344a8745efef9cc2a017024218d61c6", "sample2.idxstats:md5,69467fc02c83a30084736aeea8b785fb", "sample2.stats:md5,7cbbff1faaf2e030470a8c1e69434b48", - "somatic_smallvariants.vcf.gz:md5,1eb6db5d30ea3e1ab26685deac24983d", - "somatic_smallvariants.vcf.gz.tbi:md5,902fd2a82e6317f9e789638efacdd613", "breakpoints_double.csv:md5,d3f0957887406fb79f9dcc3707324d8c", "read_qual.txt:md5,8b92ff7dc4536188be159b95525511cd", "sample3_tumor.bam:md5,7107cfc84eafca8f1ae918e775111090", "sample3_tumor.bam.bai:md5,d2855691846361e01999895250c835e4", - "sample3_tumor_cramino.txt:md5,d3d6eecc58eb3ddd27b0a6929051b50e", "sample3.flagstat:md5,8ff32d733c62c4910bf185ef24bf27cf", "sample3.idxstats:md5,2de140e61f9e86c9c10af20dd565cc93", "sample3.stats:md5,6825d4e497aef80ed7160afbef5076d9", - "somatic_smallvariants.vcf.gz:md5,4f86dad061abc4c06481b668a2e7123f", - "somatic_smallvariants.vcf.gz.tbi:md5,b214ac172efbf09133bda2ab6b93987d", "breakpoints_double.csv:md5,41bb00e81dd6c319c13e754fa853ca68", "read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed" ] ], - "timestamp": "2026-03-13T14:09:46.004582221", + "timestamp": "2026-03-13T14:26:30.747596368", "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.4", "nextflow": "25.10.0" - }, - "timestamp": "2026-03-13T13:26:29.323724893" + } } } \ No newline at end of file