From d3431c129d28a78092146489d5054590cd2df131 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 12 Mar 2026 21:12:07 +0100 Subject: [PATCH 01/19] migrate to output for align*, qc_bam, and call* --- conf/modules/align.config | 10 ------ conf/modules/align_bwa_bwamem2_bwameme.config | 15 -------- conf/modules/align_sentieon.config | 6 ---- conf/modules/call_mobile_elements.config | 13 ------- conf/modules/call_repeat_expansions.config | 10 ------ conf/modules/call_snv.config | 11 ------ conf/modules/call_structural_variants.config | 13 ------- conf/modules/call_sv_MT.config | 13 ------- conf/modules/postprocess_MT_calls.config | 13 ------- conf/modules/qc_bam.config | 13 ------- main.nf | 10 ++++++ subworkflows/local/align/main.nf | 30 ++++++++++++++-- .../local/align_bwa_bwamem2_bwameme/main.nf | 7 ++++ subworkflows/local/align_sentieon/main.nf | 8 +++++ .../local/call_mobile_elements/main.nf | 5 +++ .../local/call_repeat_expansions/main.nf | 10 ++++-- subworkflows/local/call_snv/main.nf | 14 ++++++++ .../local/call_structural_variants/main.nf | 5 +++ subworkflows/local/call_sv_MT/main.nf | 8 +++++ .../local/postprocess_MT_calls/main.nf | 5 +++ subworkflows/local/qc_bam/main.nf | 34 +++++++++++++++++++ workflows/raredisease.nf | 20 ++++++++++- 22 files changed, 151 insertions(+), 122 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index 6df68cb32..7cc52726f 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -19,20 +19,10 @@ process{ '--correction', '--overrepresentation_analysis' ].join(' ').trim() } - publishDir = [ - path: { "${params.outdir}/trimming" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ALIGN:SAMTOOLS_VIEW' { ext.args = { '--output-fmt cram' } ext.prefix = { "${meta.id}_sort_md" } - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index d3dab330f..da2cd83ff 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -57,20 +57,5 @@ process { withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES' { ext.args = "--TMP_DIR ." ext.prefix = { "${meta.id}_sorted_md" } - publishDir = [ - enabled: !params.save_mapped_as_cram, - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP' { - publishDir = [ - enabled: !params.save_mapped_as_cram, - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/align_sentieon.config b/conf/modules/align_sentieon.config index 9a92b6057..13c051221 100644 --- a/conf/modules/align_sentieon.config +++ b/conf/modules/align_sentieon.config @@ -38,11 +38,5 @@ process { withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' { ext.args4 = { params.rmdup ? "--rmdup" : '' } ext.prefix = { "${meta.id}_dedup.bam" } - publishDir = [ - enabled: !params.save_mapped_as_cram, - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_mobile_elements.config b/conf/modules/call_mobile_elements.config index 6b1346776..dfa59f3fb 100644 --- a/conf/modules/call_mobile_elements.config +++ b/conf/modules/call_mobile_elements.config @@ -50,18 +50,5 @@ process { withName: '.*CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME' { ext.args = { '--bnd_distance 150 --overlap 0.5' } ext.prefix = { "${meta.id}_mobile_elements" } - publishDir = [ - path: { "${params.outdir}/call_mobile_elements" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*CALL_MOBILE_ELEMENTS:TABIX_ME' { - publishDir = [ - path: { "${params.outdir}/call_mobile_elements" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config index 23217bd07..916cff868 100644 --- a/conf/modules/call_repeat_expansions.config +++ b/conf/modules/call_repeat_expansions.config @@ -23,22 +23,12 @@ process { withName: '.*CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT' { ext.prefix = { "${meta.id}_exphunter_sorted" } - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' { ext.args = "--temp-prefix ." ext.args2 = "-O v" ext.prefix = { "${meta.id}_repeat_expansion" } - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } withName: '.*CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP' { diff --git a/conf/modules/call_snv.config b/conf/modules/call_snv.config index 58ad7b337..2648a2d75 100644 --- a/conf/modules/call_snv.config +++ b/conf/modules/call_snv.config @@ -16,21 +16,10 @@ process { withName: '.*CALL_SNV:GATK4_SELECTVARIANTS' { ext.args = { "--exclude-intervals ${params.mito_name}" } ext.prefix = { "${meta.id}_snv" } - publishDir = [ - path: { "${params.outdir}/call_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*CALL_SNV:BCFTOOLS_CONCAT' { ext.args = { "--write-index=tbi" } ext.prefix = { "${meta.id}_mt_and_nuclear_snvs" } - publishDir = [ - enabled: params.concatenate_snv_calls, - path: { "${params.outdir}/call_snv/concatenated_calls" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_structural_variants.config b/conf/modules/call_structural_variants.config index 23e9325b6..a9fcd660d 100644 --- a/conf/modules/call_structural_variants.config +++ b/conf/modules/call_structural_variants.config @@ -20,18 +20,5 @@ process { withName: '.*CALL_STRUCTURAL_VARIANTS:SVDB_MERGE' { ext.prefix = {"${meta.id}_sv"} ext.args = '--pass_only --same_order' - publishDir = [ - path: { "${params.outdir}/call_sv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*CALL_STRUCTURAL_VARIANTS:TABIX_TABIX' { - publishDir = [ - path: { "${params.outdir}/call_sv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index deedd506d..be140cabe 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -20,19 +20,6 @@ process { withName: '.*CALL_SV_MT:MT_DELETION' { ext.args = '-s --insert-size 16000' ext.prefix = { "${meta.id}_mitochondria_deletions" } - publishDir = [ - path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*CALL_SV_MT:MITOSALT' { - publishDir = [ - path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/postprocess_MT_calls.config b/conf/modules/postprocess_MT_calls.config index 61a14131a..f54c383e6 100644 --- a/conf/modules/postprocess_MT_calls.config +++ b/conf/modules/postprocess_MT_calls.config @@ -47,19 +47,6 @@ process { withName: '.*POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE' { ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z --include FILTER='\"PASS\"'" ext.prefix = { "${meta.id}_mitochondria" } - publishDir = [ - path: { "${params.outdir}/call_snv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*POSTPROCESS_MT_CALLS:TABIX_ANNOTATE' { - publishDir = [ - path: { "${params.outdir}/call_snv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index 0b49f6c80..d0905762b 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -16,14 +16,6 @@ // process { - withName: '.*QC_BAM:.*' { - publishDir = [ - path: { "${params.outdir}/qc_bam" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - } - withName: '.*QC_BAM:PICARD_COLLECTMULTIPLEMETRICS' { ext.args = "--TMP_DIR ." ext.prefix = { "${meta.id}_multiplemetrics" } @@ -61,11 +53,6 @@ process { // NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } ext.prefix = { "${meta.id}_ngsbits_sex" } - publishDir = [ - path: { "${params.outdir}/ngsbits_samplegender" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_WG' { diff --git a/main.nf b/main.nf index 5346dbd30..58cb974b8 100644 --- a/main.nf +++ b/main.nf @@ -466,6 +466,7 @@ workflow NFCORE_RAREDISEASE { ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + ch_publish = RAREDISEASE.out.ch_publish // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -586,6 +587,15 @@ workflow { params.hook_url, NFCORE_RAREDISEASE.out.multiqc_report ) + + publish: + subworkflow_results = NFCORE_RAREDISEASE.out.ch_publish +} + +output { + subworkflow_results { + path { destination, value -> destination } + } } /* diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index cc9cf0b9f..65b97acf1 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -45,17 +45,26 @@ workflow ALIGN { ch_bwamem2_bam = channel.empty() ch_bwamem2_bai = channel.empty() ch_fastp_json = channel.empty() + ch_fastp_publish = channel.empty() ch_markdup_metrics = channel.empty() ch_mt_bam_bai = channel.empty() ch_mt_bam_bai_gatksubwf = channel.empty() ch_mtshift_bam_bai_gatksubwf = channel.empty() ch_sentieon_bam = channel.empty() ch_sentieon_bai = channel.empty() + ch_cram_publish = channel.empty() if (!skip_fastp) { FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) - ch_input_reads = FASTP.out.reads - ch_fastp_json = FASTP.out.json + ch_input_reads = FASTP.out.reads + ch_fastp_json = FASTP.out.json + ch_fastp_publish = FASTP.out.json + .mix(FASTP.out.html) + .mix(FASTP.out.log) + .mix(FASTP.out.reads) + .mix(FASTP.out.reads_fail) + .mix(FASTP.out.reads_merged) + .map { meta, value -> ['trimming/', [meta, value]] } } // @@ -152,8 +161,24 @@ workflow ALIGN { if (val_save_mapped_as_cram) { SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) + ch_cram_publish = SAMTOOLS_VIEW.out.cram + .mix(SAMTOOLS_VIEW.out.crai) + .map { meta, value -> ['alignment/', [meta, value]] } } + ch_bam_publish = channel.empty() + if (!val_save_mapped_as_cram) { + if (val_aligner.matches("bwamem2|bwa|bwameme")) { + ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.ch_publish + } else if (val_aligner.equals("sentieon")) { + ch_bam_publish = ALIGN_SENTIEON.out.ch_publish + } + } + + ch_publish = ch_fastp_publish + .mix(ch_bam_publish) + .mix(ch_cram_publish) + emit: fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] @@ -163,4 +188,5 @@ workflow ALIGN { mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 615e6b1ad..fda97a2c3 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -77,9 +77,16 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { MARKDUPLICATES ( prepared_bam , ch_genome_fasta, ch_genome_fai ) SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) + ch_publish = MARKDUPLICATES.out.bam + .mix(MARKDUPLICATES.out.metrics) + .mix(SAMTOOLS_INDEX_MARKDUP.out.bai) + .mix(SAMTOOLS_INDEX_MARKDUP.out.csi) + .map { meta, value -> ['alignment/', [meta, value]] } + emit: marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index b115efa41..74b1cc1f2 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -48,6 +48,13 @@ workflow ALIGN_SENTIEON { SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai ) + ch_publish = SENTIEON_DEDUP.out.bam + .mix(SENTIEON_DEDUP.out.bai) + .mix(SENTIEON_DEDUP.out.score) + .mix(SENTIEON_DEDUP.out.metrics) + .mix(SENTIEON_DEDUP.out.metrics_multiqc_tsv) + .map { meta, value -> ['alignment/', [meta, value]] } + emit: marked_bam = SENTIEON_DEDUP.out.bam // channel: [ val(meta), path(bam) ] marked_bai = SENTIEON_DEDUP.out.bai // channel: [ val(meta), path(bai) ] @@ -57,4 +64,5 @@ workflow ALIGN_SENTIEON { gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_mobile_elements/main.nf b/subworkflows/local/call_mobile_elements/main.nf index 06cd34a5c..80c4bc696 100644 --- a/subworkflows/local/call_mobile_elements/main.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -119,7 +119,12 @@ workflow CALL_MOBILE_ELEMENTS { SVDB_MERGE_ME ( ch_svdb_merge_me_input, [], true ) TABIX_ME ( SVDB_MERGE_ME.out.vcf ) + ch_publish = SVDB_MERGE_ME.out.vcf + .mix(TABIX_ME.out.index) + .map { meta, value -> ['call_mobile_elements/', [meta, value]] } + emit: tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 14ec4fb61..ea6d82010 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -57,6 +57,12 @@ workflow CALL_REPEAT_EXPANSIONS { SVDB_MERGE_REPEATS ( ch_svdb_merge_input, [], true ) -emit: - vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish = SAMTOOLS_SORT.out.bam + .mix(SAMTOOLS_SORT.out.bai) + .mix(BCFTOOLS_REHEADER_EXP.out.vcf) + .map { meta, value -> ['repeat_expansions/', [meta, value]] } + + emit: + vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index dad2ce611..acc607efb 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -53,6 +53,8 @@ workflow CALL_SNV { ch_sentieon_tbi = channel.empty() ch_sentieon_gvcf = channel.empty() ch_sentieon_gtbi = channel.empty() + ch_concat_publish = channel.empty() + ch_mt_snv_publish = channel.empty() if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( @@ -136,6 +138,7 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) + ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.ch_publish } if (val_concatenate_snv_calls) { @@ -143,8 +146,18 @@ workflow CALL_SNV { BCFTOOLS_CONCAT ( ch_concat_vcf_in ) + ch_concat_publish = BCFTOOLS_CONCAT.out.vcf + .mix(BCFTOOLS_CONCAT.out.tbi) + .mix(BCFTOOLS_CONCAT.out.csi) + .map { meta, value -> ['call_snv/concatenated_calls/', [meta, value]] } } + ch_publish = GATK4_SELECTVARIANTS.out.vcf + .mix(GATK4_SELECTVARIANTS.out.tbi) + .map { meta, value -> ['call_snv/genome/', [meta, value]] } + .mix(ch_concat_publish) + .mix(ch_mt_snv_publish) + emit: genome_gtabix = ch_gtabix // channel: [ val(meta), path(gtbi) ] genome_gvcf = ch_gvcf // channel: [ val(meta), path(gvcf) ] @@ -153,4 +166,5 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 62ddf1a97..49c062ee7 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -98,7 +98,12 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_merged_tbi = TABIX_TABIX.out.index } + ch_publish = ch_merged_svs + .mix(ch_merged_tbi) + .map { meta, value -> ['call_sv/genome/', [meta, value]] } + emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index f24d752fc..5c7a97913 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -36,6 +36,7 @@ workflow CALL_SV_MT { val_split_length // string: [mandatory] mitosalt_split_length main: + ch_mitosalt_publish = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -76,12 +77,19 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) + ch_mitosalt_publish = MITOSALT.out.breakpoint + .mix(MITOSALT.out.cluster) } MT_DELETION(ch_bam_bai, ch_genome_fasta) + ch_publish = ch_mitosalt_publish + .mix(MT_DELETION.out.mt_del_result) + .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } + emit: mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 388aaab1a..9f631cd5f 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -120,7 +120,12 @@ workflow POSTPROCESS_MT_CALLS { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) + ch_publish = BCFTOOLS_ANNOTATE.out.vcf + .mix(TABIX_ANNOTATE.out.index) + .map { meta, value -> ['call_snv/mitochondria/', [meta, value]] } + emit: tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index d2edb0da1..307c51b4e 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -96,6 +96,39 @@ workflow QC_BAM { ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) + ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) + .mix(TIDDIT_COV.out.wig) + .mix(TIDDIT_COV.out.cov) + .mix(UCSC_WIGTOBIGWIG.out.bw) + .mix(CHROMOGRAPH_COV.out.plots) + .mix(MOSDEPTH.out.global_txt) + .mix(MOSDEPTH.out.summary_txt) + .mix(MOSDEPTH.out.per_base_d4) + .mix(MOSDEPTH.out.regions_txt) + .mix(MOSDEPTH.out.per_base_bed) + .mix(MOSDEPTH.out.per_base_csi) + .mix(MOSDEPTH.out.regions_bed) + .mix(MOSDEPTH.out.regions_csi) + .mix(MOSDEPTH.out.quantized_bed) + .mix(MOSDEPTH.out.quantized_csi) + .mix(MOSDEPTH.out.thresholds_bed) + .mix(MOSDEPTH.out.thresholds_csi) + .mix(SAMBAMBA_DEPTH.out.bed) + .mix(VERIFYBAMID_VERIFYBAMID2.out.self_sm) + .mix(VERIFYBAMID_VERIFYBAMID2.out.log) + .mix(VERIFYBAMID_VERIFYBAMID2.out.ud) + .mix(VERIFYBAMID_VERIFYBAMID2.out.bed) + .mix(VERIFYBAMID_VERIFYBAMID2.out.mu) + .mix(VERIFYBAMID_VERIFYBAMID2.out.ancestry) + .mix(ch_hsmetrics) + .mix(ch_qualimap) + .mix(ch_cov) + .mix(ch_cov_y) + .map { meta, value -> ['qc_bam/', [meta, value]] } + .mix(ch_ngsbits + .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] }) + emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] @@ -108,4 +141,5 @@ workflow QC_BAM { self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] cov = ch_cov // channel: [ val(meta), path(metrics) ] cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3d400bd61..e81a3429b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -205,7 +205,12 @@ workflow RAREDISEASE { main: - ch_multiqc_files = channel.empty() + ch_multiqc_files = channel.empty() + ch_call_snv_publish = channel.empty() + ch_call_sv_publish = channel.empty() + ch_call_sv_mt_publish = channel.empty() + ch_call_repeat_expansions_publish = channel.empty() + ch_call_mobile_elements_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -337,6 +342,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai ) + ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.ch_publish if (!skip_repeat_annotation) { STRANGER ( @@ -384,6 +390,7 @@ workflow RAREDISEASE { val_run_mt_for_wes, val_variant_caller ) + ch_call_snv_publish = CALL_SNV.out.ch_publish // // ANNOTATE GENOME SNVs @@ -550,6 +557,8 @@ workflow RAREDISEASE { val_analysis_type, skip_germlinecnvcaller, ) + ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.ch_publish + // // ANNOTATE STRUCTURAL VARIANTS // @@ -646,6 +655,7 @@ workflow RAREDISEASE { params.split_distance_threshold, params.split_length ) + ch_call_sv_mt_publish = CALL_SV_MT.out.ch_publish } /* @@ -662,6 +672,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_me_references ) + ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.ch_publish if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( @@ -893,6 +904,13 @@ workflow RAREDISEASE { emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + ch_publish = ALIGN.out.ch_publish + .mix(QC_BAM.out.ch_publish) + .mix(ch_call_snv_publish) + .mix(ch_call_sv_publish) + .mix(ch_call_sv_mt_publish) + .mix(ch_call_repeat_expansions_publish) + .mix(ch_call_mobile_elements_publish) // channel: [ val(destination), val(value) ] } From cbfbb344f9d2e970b4a85b00b590b2aff97ac68e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 12 Mar 2026 22:19:19 +0100 Subject: [PATCH 02/19] updaate changelog --- CHANGELOG.md | 1 + nextflow.config | 2 ++ 2 files changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02b3eedb3..0a0363cc0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -36,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) - Removed HmtNote [#779](https://github.com/nf-core/raredisease/pull/779) - Updated svbd module [#781](https://github.com/nf-core/raredisease/pull/781) +- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#784](https://github.com/nf-core/raredisease/pull/784) ### `Fixed` diff --git a/nextflow.config b/nextflow.config index bd520863d..4c212227e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -175,6 +175,8 @@ params { validate_params = true } +workflow.output.mode = 'copy' + // Load base.config by default for all pipelines includeConfig 'conf/base.config' From 9178577eaab61a75ded35e9675e66f332496d149 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 10:09:42 +0100 Subject: [PATCH 03/19] update tests and snaps --- NEXTFLOW_OUTPUT_MIGRATION.md | 162 +++ main.nf | 4 +- subworkflows/local/align/main.nf | 6 +- subworkflows/local/align/tests/main.nf.test | 3 + .../local/align/tests/main.nf.test.snap | 927 +++++++++++++++++- .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- .../tests/main.nf.test | 2 + .../tests/main.nf.test.snap | 104 +- subworkflows/local/align_sentieon/main.nf | 2 +- .../local/call_mobile_elements/main.nf | 2 +- .../tests/main.nf.test.snap | 42 +- .../local/call_repeat_expansions/main.nf | 2 +- .../call_repeat_expansions/tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 65 +- subworkflows/local/call_snv/main.nf | 4 +- .../local/call_snv/tests/main.nf.test | 1 + .../local/call_snv/tests/main.nf.test.snap | 118 ++- .../local/call_structural_variants/main.nf | 2 +- .../tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 22 +- subworkflows/local/call_sv_MT/main.nf | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 120 ++- .../local/postprocess_MT_calls/main.nf | 2 +- .../tests/main.nf.test.snap | 42 +- subworkflows/local/qc_bam/main.nf | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 2 + tests/default.nf.test.snap | 386 +------- tests/test_bam.nf.test.snap | 355 +------ tests/test_singleton.nf.test.snap | 142 +-- workflows/raredisease.nf | 18 +- 30 files changed, 1627 insertions(+), 916 deletions(-) create mode 100644 NEXTFLOW_OUTPUT_MIGRATION.md diff --git a/NEXTFLOW_OUTPUT_MIGRATION.md b/NEXTFLOW_OUTPUT_MIGRATION.md new file mode 100644 index 000000000..c8a408161 --- /dev/null +++ b/NEXTFLOW_OUTPUT_MIGRATION.md @@ -0,0 +1,162 @@ +--- + +## Centralized Publishing Pattern (nf-core migration approach) + +Instead of using `topic` channels or `publishDir`, we use a **single `ch_publish` channel +per subworkflow** that emits `[destination, value]` tuples. Publishing is handled centrally +in `main.nf`. + +### Pattern Overview + +**Inside each subworkflow**, map every published output into a `[destination, value]` tuple +where `destination` mirrors the original `publishDir` path. Mix all of them into a single +`ch_publish` and emit it: + +```nextflow +// Inside subworkflow +ch_publish = PROCESS_A.out.bam + .map { meta, bam -> ['alignment/', [meta, bam]] } + .mix(PROCESS_B.out.metrics.map { meta, f -> ['qc/', [meta, f]] }) + .mix(PROCESS_C.out.vcf.map { meta, vcf -> ['vcf/', [meta, vcf]] }) + +emit: +ch_publish +``` + +Rules: + +- There must be only **one `ch_publish` emit per subworkflow** +- The destination string should mirror the original `publishDir` path +- Preserve the original channel structure as the second element of the tuple +- Include outputs from processes whose channels are not consumed downstream — + these were previously captured by `publishDir` at the filesystem level + +**In `main.nf`**, collect `ch_publish` from all subworkflows, mix them, and publish +centrally: + +```nextflow +workflow { + main: + SUBWORKFLOW_A(...) + SUBWORKFLOW_B(...) + + publish: + all_outputs = SUBWORKFLOW_A.out.ch_publish + .mix(SUBWORKFLOW_B.out.ch_publish) +} + +output { + all_outputs { + path { destination, value -> destination } + } +} +``` + +### Handling varying channel structures + +Channels with different numbers of elements (e.g. `[meta, bam]` vs `[meta, bam, bai]`) +are handled safely by always wrapping the entire inner tuple as a single second element. +Nextflow recursively scans the value for file objects automatically. + +// CORRECT +.map { meta, bam, bai -> ['alignment/', [meta, bam, bai]] } + +// WRONG — breaks the [destination, value] contract +.map { meta, bam, bai -> ['alignment/', meta, bam, bai] } +``` + +**Your command** — add one line to enforce the wrapping rule: +``` +... + +For each process output that should be published, map it into a tuple of +[destination_path, channel_value] where destination_path mirrors the directory +that publishDir was publishing to. Always wrap the entire channel value as a +single second element regardless of how many elements it contains, e.g. +{ meta, bam, bai -> ['alignment/', [meta, bam, bai]] }. +... + +### Grouping channels by destination before mapping + +Instead of mapping each channel individually, group channels sharing the same destination +using `mix` first, then apply a single `map` per destination group. This reduces repetition +significantly. + +```nextflow +// PREFERRED — one map per destination group +ch_qc_bam = PICARD_COLLECTMULTIPLEMETRICS.out.metrics + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) + .mix(TIDDIT_COV.out.wig) + .mix(MOSDEPTH.out.global_txt) + .mix(ch_qualimap) + .map { meta, value -> ['qc_bam/', [meta, value]] } + +ch_ngsbits = ch_ngsbits_samplegender + .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] } + +ch_publish = ch_qc_bam.mix(ch_ngsbits) + +// AVOID — one map per channel, very repetitive +ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics + .map { meta, metrics -> ['qc_bam/', [meta, metrics]] } + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf + .map { meta, pdf -> ['qc_bam/', [meta, pdf]] }) + // ... +``` + +Rules: + +- Create one intermediate channel per unique destination directory +- Mix all channels going to the same destination first, then apply a single `map` +- Combine all destination groups into `ch_publish` with a final `mix` + +### Nested subworkflows — bubbling up ch_publish + +When a subworkflow calls other subworkflows, always mix the inner `ch_publish` into the +outer `ch_publish`. This propagates publishing up the call chain to `main.nf`. + +```nextflow +// Inner subworkflow emits its own ch_publish +workflow ALIGN_BWA { + main: + BWA_MEM(...) + SAMTOOLS_SORT(...) + + ch_publish = BWA_MEM.out.bam + .mix(SAMTOOLS_SORT.out.bam) + .map { meta, value -> ['alignment/', [meta, value]] } + + emit: + ch_publish +} + +// Outer subworkflow mixes in ch_publish from inner subworkflow +workflow ALIGN { + main: + ALIGN_BWA(...) + FASTP(...) + + ch_publish = FASTP.out.reads + .map { meta, value -> ['fastp/', [meta, value]] } + .mix(ALIGN_BWA.out.ch_publish) + + emit: + ch_publish +} +``` + +Rules: + +- Every subworkflow that has publishable outputs must emit `ch_publish` +- If a subworkflow calls inner subworkflows, always mix their `ch_publish` into the + outer `ch_publish` — never discard it +- In `main.nf`, mix `ch_publish` from all top-level subworkflows into one channel + before the `publish:` block + +### Why this approach + +- Subworkflow signatures stay clean — one `ch_publish` emit regardless of how many + output directories exist internally +- Publishing logic is fully centralized in `main.nf` +- No `topic` channel footguns (pipeline hanging forever if a process consumes its own topic) +- Easy to audit all published paths by reading `main.nf` alone diff --git a/main.nf b/main.nf index 58cb974b8..f36c819a1 100644 --- a/main.nf +++ b/main.nf @@ -466,7 +466,7 @@ workflow NFCORE_RAREDISEASE { ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - ch_publish = RAREDISEASE.out.ch_publish // channel: [ val(destination), val(value) ] + publish = RAREDISEASE.out.publish // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -589,7 +589,7 @@ workflow { ) publish: - subworkflow_results = NFCORE_RAREDISEASE.out.ch_publish + subworkflow_results = NFCORE_RAREDISEASE.out.publish } output { diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 65b97acf1..f61c92e04 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -169,9 +169,9 @@ workflow ALIGN { ch_bam_publish = channel.empty() if (!val_save_mapped_as_cram) { if (val_aligner.matches("bwamem2|bwa|bwameme")) { - ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.ch_publish + ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.publish } else if (val_aligner.equals("sentieon")) { - ch_bam_publish = ALIGN_SENTIEON.out.ch_publish + ch_bam_publish = ALIGN_SENTIEON.out.publish } } @@ -188,5 +188,5 @@ workflow ALIGN { mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index dce17b191..06df3a019 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -116,6 +116,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -216,6 +217,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -308,6 +310,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index ceb34df54..93aa1301f 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -1,6 +1,371 @@ { "align bwamem2 - wgs": { "content": [ + [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sort_md.cram:md5,bc7f10d51c282f5632a7fce6a76a891a" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sort_md.cram.crai:md5,b72dd8b4097b1adef34747aa2c53a3ca" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sort_md.cram:md5,6e7b8b26c4e3851fa1f4bf4a629016d9" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sort_md.cram.crai:md5,e39b6adfff50427d53f7e8cd43b1cd26" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sort_md.cram:md5,b34cfc30ca2754d70e69fabadefba4d7" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sort_md.cram.crai:md5,34cc581f4684ba2f403bc1eea3975ad7" + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "slowlycivilbuck_R1.fastp.fastq.gz:md5,34b043eb99b2f0f4369079d90dd09b5c", + "slowlycivilbuck_R2.fastp.fastq.gz:md5,54520d9ce8ccd2f54cec2873bbaed0ed" + ] + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.log:md5,17d946e68aee1f92ae5334a74fde8571" + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.json:md5,7ad34e9e48159c794ce777e4e48c0b96" + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.html:md5,78c27a84b0667febcb848c83e35eada1" + ] + ], + [ + "trimming/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + 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"sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "trimming/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "trimming/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "trimming/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], [ [ { @@ -445,7 +1366,7 @@ ] ], - "timestamp": "2026-02-17T14:53:17.634008549", + "timestamp": "2026-03-13T09:09:46.038355114", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index fda97a2c3..66eafb804 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -88,5 +88,5 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index cdde33d3e..13fdcdf2a 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -55,6 +55,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -111,6 +112,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 09b3ed99d..c61fe2bb9 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -1,6 +1,56 @@ { "align bwamem2": { "content": [ + [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,171423ac03499a00c4677f8b53771570" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,4730bcc5e26e8f3c29b8fa58f68d43e6" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,b8976cf366140eeee478ee2e9c1cadc9" + ] + ] + ], [ [ { @@ -32,7 +82,7 @@ ] ] ], - "timestamp": "2026-02-27T15:46:37.232286266", + "timestamp": "2026-03-13T09:21:28.631120006", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -40,6 +90,56 @@ }, "align bwameme": { "content": [ + [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,ca247f01365899e07c77c3479fa721b2" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,f5b5580ca2b1035f0cac8ba1db7ab55e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,e1e422e8da8ae8f2fbf0221d29919be0" + ] + ] + ], [ [ { @@ -71,7 +171,7 @@ ] ] ], - "timestamp": "2026-02-27T15:47:22.733461874", + "timestamp": "2026-03-13T09:22:14.004999114", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 74b1cc1f2..2038682b5 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -64,5 +64,5 @@ workflow ALIGN_SENTIEON { gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_mobile_elements/main.nf b/subworkflows/local/call_mobile_elements/main.nf index 80c4bc696..896da1068 100644 --- a/subworkflows/local/call_mobile_elements/main.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -126,5 +126,5 @@ workflow CALL_MOBILE_ELEMENTS { emit: tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap index 9ce36a3b4..bf9b9c3a3 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap @@ -18,6 +18,46 @@ "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "2": [ + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "publish": [ + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -36,7 +76,7 @@ ] } ], - "timestamp": "2026-03-04T15:43:58.250066806", + "timestamp": "2026-03-13T09:28:04.925769836", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index ea6d82010..a3bac56e0 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -64,5 +64,5 @@ workflow CALL_REPEAT_EXPANSIONS { emit: vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 75b99f949..8664d596f 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_workflow { then { assert workflow.success assert snapshot( + workflow.out.publish, path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 685492b45..a69390d12 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -1,13 +1,72 @@ { "CALL_REPEAT_EXPANSIONS": { "content": [ + [ + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,9e2d2ec1df32e12dc2e043f7f5dae61c" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,32e22328efec8cdd3c818e18568f2108" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,7cdcf4e866373d4aa0e762acfe0f5d5a" + ] + ] + ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2025-10-14T14:06:58.984015651", + "timestamp": "2026-03-13T09:28:35.853691152", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index acc607efb..266ec9881 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -138,7 +138,7 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) - ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.ch_publish + ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.publish } if (val_concatenate_snv_calls) { @@ -166,5 +166,5 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 35cdbda99..727903fdf 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -59,6 +59,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index baf3c72ff..c8a7b4c10 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -1,6 +1,44 @@ { "CALL_SNV - deepvariant wgs": { "content": [ + [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,b78d7a388ac51028ca8b15474b9efce6" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,81c8e362552865ccdd12941db07bdf6e" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,5b31cdd1aaca1b52aa06ec49b0d3207f" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,057840edb22fe608c7635911a914e9f0" + ] + ] + ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ @@ -10,7 +48,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-04T15:51:36.199641201", + "timestamp": "2026-03-13T09:33:27.081509863", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -96,6 +134,44 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "7": [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "genome_gtabix": [ [ { @@ -172,10 +248,48 @@ }, "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] + ], + "publish": [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-09T11:14:37.035323634", + "timestamp": "2026-03-13T09:34:33.930010907", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 49c062ee7..c6588e55e 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -105,5 +105,5 @@ workflow CALL_STRUCTURAL_VARIANTS { emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 139d26d58..26b2f362b 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -46,6 +46,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 2577e99f7..999d3184e 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -1,6 +1,26 @@ { "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ + [ + [ + "call_sv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_sv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], [ "justhusky_sv.vcf.gz" ], @@ -8,7 +28,7 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-01T18:18:21.549692378", + "timestamp": "2026-03-13T09:44:18.163494369", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 5c7a97913..5b74b7ba2 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -91,5 +91,5 @@ workflow CALL_SV_MT { mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index e40ea67d7..dc0f6c7af 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -56,6 +56,65 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "3": [ + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "mitosalt_breakpoint": [ [ { @@ -109,10 +168,69 @@ }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "publish": [ + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-06T06:08:49.770501228", + "timestamp": "2026-03-13T09:44:41.052362674", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 9f631cd5f..ef10982ec 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -127,5 +127,5 @@ workflow POSTPROCESS_MT_CALLS { emit: tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap index bd5f6421c..fa37649d4 100644 --- a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap @@ -18,6 +18,46 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "2": [ + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "ch_publish": [ + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -36,7 +76,7 @@ ] } ], - "timestamp": "2026-03-05T22:02:56.111310181", + "timestamp": "2026-03-12T23:41:04.472222425", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 307c51b4e..35d00c4d4 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -141,5 +141,5 @@ workflow QC_BAM { self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] cov = ch_cov // channel: [ val(meta), path(metrics) ] cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index f97d7b47a..f354e408c 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -54,6 +54,7 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.multiple_metrics .collect {it[1]} .flatten() @@ -132,6 +133,7 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.multiple_metrics .collect {it[1]} .flatten() diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ce8cf8ed1..538aa9fcc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -502,19 +502,10 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", - "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/hugelymodelbat_sorted_md.metrics.txt", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", - "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -669,30 +660,6 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", - "call_mobile_elements", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", - "call_snv", - "call_snv/genome", - "call_snv/genome/justhusky_snv.vcf.gz", - "call_snv/genome/justhusky_snv.vcf.gz.tbi", - "call_snv/mitochondria", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", - "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -708,10 +675,6 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", - "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", - "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -727,328 +690,6 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", - "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - "qc_bam/earlycasualcaiman/css/doctools.js", - "qc_bam/earlycasualcaiman/css/down-pressed.png", - "qc_bam/earlycasualcaiman/css/down.png", - "qc_bam/earlycasualcaiman/css/file.png", - "qc_bam/earlycasualcaiman/css/jquery.js", - "qc_bam/earlycasualcaiman/css/minus.png", - "qc_bam/earlycasualcaiman/css/plus.png", - "qc_bam/earlycasualcaiman/css/pygments.css", - "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", - "qc_bam/earlycasualcaiman/css/report.css", - "qc_bam/earlycasualcaiman/css/searchtools.js", - "qc_bam/earlycasualcaiman/css/underscore.js", - "qc_bam/earlycasualcaiman/css/up-pressed.png", - "qc_bam/earlycasualcaiman/css/up.png", - "qc_bam/earlycasualcaiman/css/websupport.js", - "qc_bam/earlycasualcaiman/genome_results.txt", - "qc_bam/earlycasualcaiman/images_qualimapReport", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", - 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"qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -1008,17 +664,8 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -1029,7 +676,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-10T15:54:35.091523871", + "timestamp": "2026-03-12T22:43:18.380887473", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 0e6dfba4d..f23ae4108 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -485,9 +485,6 @@ "alignment", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -534,24 +531,6 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", - "call_mobile_elements", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", - "call_snv", - "call_snv/genome", - "call_snv/genome/justhusky_snv.vcf.gz", - "call_snv/genome/justhusky_snv.vcf.gz.tbi", - "call_snv/mitochondria", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", - "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -561,8 +540,6 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", - "ngsbits_samplegender", - "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -578,114 +555,6 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", - "qc_bam", - "qc_bam/hugelymodelbat", - "qc_bam/hugelymodelbat/css", - "qc_bam/hugelymodelbat/css/agogo.css", - "qc_bam/hugelymodelbat/css/ajax-loader.gif", - "qc_bam/hugelymodelbat/css/basic.css", - "qc_bam/hugelymodelbat/css/bgfooter.png", - "qc_bam/hugelymodelbat/css/bgtop.png", - "qc_bam/hugelymodelbat/css/comment-bright.png", - "qc_bam/hugelymodelbat/css/comment-close.png", - "qc_bam/hugelymodelbat/css/comment.png", - "qc_bam/hugelymodelbat/css/doctools.js", - "qc_bam/hugelymodelbat/css/down-pressed.png", - "qc_bam/hugelymodelbat/css/down.png", - "qc_bam/hugelymodelbat/css/file.png", - "qc_bam/hugelymodelbat/css/jquery.js", - "qc_bam/hugelymodelbat/css/minus.png", - "qc_bam/hugelymodelbat/css/plus.png", - "qc_bam/hugelymodelbat/css/pygments.css", - "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", - "qc_bam/hugelymodelbat/css/report.css", - "qc_bam/hugelymodelbat/css/searchtools.js", - "qc_bam/hugelymodelbat/css/underscore.js", - "qc_bam/hugelymodelbat/css/up-pressed.png", - "qc_bam/hugelymodelbat/css/up.png", - "qc_bam/hugelymodelbat/css/websupport.js", - "qc_bam/hugelymodelbat/genome_results.txt", - "qc_bam/hugelymodelbat/images_qualimapReport", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/hugelymodelbat/qualimapReport.html", - "qc_bam/hugelymodelbat/raw_data_qualimapReport", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.per-base.d4", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.summary.txt", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/hugelymodelbat_tidditcov.bed", - "qc_bam/hugelymodelbat_tidditcov.bw", - "qc_bam/hugelymodelbat_tidditcov.wig", - "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", - "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -700,26 +569,17 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-10T15:15:02.654289867", + "timestamp": "2026-03-12T22:47:05.119730547", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index e81a3429b..8d78db201 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -206,6 +206,8 @@ workflow RAREDISEASE { main: ch_multiqc_files = channel.empty() + ch_align_publish = channel.empty() + ch_qc_bam_publish = channel.empty() ch_call_snv_publish = channel.empty() ch_call_sv_publish = channel.empty() ch_call_sv_mt_publish = channel.empty() @@ -278,6 +280,7 @@ workflow RAREDISEASE { val_save_mapped_as_cram ) .set { ch_mapped } + ch_align_publish = ALIGN.out.publish if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || val_run_mt_for_wes)) { if (val_mt_subsample_approach.equals("fraction")) { @@ -317,6 +320,7 @@ workflow RAREDISEASE { skip_ngsbits, skip_qualimap ) + ch_qc_bam_publish = QC_BAM.out.publish /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -342,7 +346,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai ) - ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.ch_publish + ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.publish if (!skip_repeat_annotation) { STRANGER ( @@ -390,7 +394,7 @@ workflow RAREDISEASE { val_run_mt_for_wes, val_variant_caller ) - ch_call_snv_publish = CALL_SNV.out.ch_publish + ch_call_snv_publish = CALL_SNV.out.publish // // ANNOTATE GENOME SNVs @@ -557,7 +561,7 @@ workflow RAREDISEASE { val_analysis_type, skip_germlinecnvcaller, ) - ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.ch_publish + ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish // // ANNOTATE STRUCTURAL VARIANTS @@ -655,7 +659,7 @@ workflow RAREDISEASE { params.split_distance_threshold, params.split_length ) - ch_call_sv_mt_publish = CALL_SV_MT.out.ch_publish + ch_call_sv_mt_publish = CALL_SV_MT.out.publish } /* @@ -672,7 +676,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_me_references ) - ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.ch_publish + ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.publish if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( @@ -904,8 +908,8 @@ workflow RAREDISEASE { emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] - ch_publish = ALIGN.out.ch_publish - .mix(QC_BAM.out.ch_publish) + publish = ch_align_publish + .mix(ch_qc_bam_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) .mix(ch_call_sv_mt_publish) From aa5f8761cf1eb799367f2a31782c837c67345fbc Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 11:16:12 +0100 Subject: [PATCH 04/19] update snapshot --- .../align_sentieon/tests/main.nf.test.snap | 170 ++++- .../local/qc_bam/tests/main.nf.test.snap | 634 +++++++++++++++++- 2 files changed, 799 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 79a96bf5a..9b1ad860b 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -122,6 +122,88 @@ "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" ] ], + "8": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + ] + ] + ], "aln_metrics": [ [ { @@ -227,6 +309,88 @@ "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" ] ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", 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"earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics:md5,f6167a1a32ca549756dc253ba8891300" + ] + ] + ], + [ + "qc_bam/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics:md5,d4c02430a4ec0dc6c9a1b6b7ad89ac46" + ] + ] + ], [ "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", @@ -151,7 +781,7 @@ ] ] ], - "timestamp": "2026-02-17T15:21:49.953972761", + "timestamp": "2026-03-13T11:15:12.139419029", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 5788ace5b1a381b6a9f7c8dee4d815d343144393 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 14:02:33 +0100 Subject: [PATCH 05/19] update snapshots --- NEXTFLOW_OUTPUT_MIGRATION.md | 162 --- subworkflows/local/align/tests/main.nf.test | 12 +- .../local/align/tests/main.nf.test.snap | 972 +----------------- .../tests/main.nf.test | 8 +- .../tests/main.nf.test.snap | 106 +- .../call_repeat_expansions/tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 62 +- .../local/call_snv/tests/main.nf.test | 4 +- .../local/call_snv/tests/main.nf.test.snap | 42 +- .../tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 22 +- subworkflows/local/qc_bam/tests/main.nf.test | 8 +- .../local/qc_bam/tests/main.nf.test.snap | 63 +- 13 files changed, 111 insertions(+), 1358 deletions(-) delete mode 100644 NEXTFLOW_OUTPUT_MIGRATION.md diff --git a/NEXTFLOW_OUTPUT_MIGRATION.md b/NEXTFLOW_OUTPUT_MIGRATION.md deleted file mode 100644 index c8a408161..000000000 --- a/NEXTFLOW_OUTPUT_MIGRATION.md +++ /dev/null @@ -1,162 +0,0 @@ ---- - -## Centralized Publishing Pattern (nf-core migration approach) - -Instead of using `topic` channels or `publishDir`, we use a **single `ch_publish` channel -per subworkflow** that emits `[destination, value]` tuples. Publishing is handled centrally -in `main.nf`. - -### Pattern Overview - -**Inside each subworkflow**, map every published output into a `[destination, value]` tuple -where `destination` mirrors the original `publishDir` path. Mix all of them into a single -`ch_publish` and emit it: - -```nextflow -// Inside subworkflow -ch_publish = PROCESS_A.out.bam - .map { meta, bam -> ['alignment/', [meta, bam]] } - .mix(PROCESS_B.out.metrics.map { meta, f -> ['qc/', [meta, f]] }) - .mix(PROCESS_C.out.vcf.map { meta, vcf -> ['vcf/', [meta, vcf]] }) - -emit: -ch_publish -``` - -Rules: - -- There must be only **one `ch_publish` emit per subworkflow** -- The destination string should mirror the original `publishDir` path -- Preserve the original channel structure as the second element of the tuple -- Include outputs from processes whose channels are not consumed downstream — - these were previously captured by `publishDir` at the filesystem level - -**In `main.nf`**, collect `ch_publish` from all subworkflows, mix them, and publish -centrally: - -```nextflow -workflow { - main: - SUBWORKFLOW_A(...) - SUBWORKFLOW_B(...) - - publish: - all_outputs = SUBWORKFLOW_A.out.ch_publish - .mix(SUBWORKFLOW_B.out.ch_publish) -} - -output { - all_outputs { - path { destination, value -> destination } - } -} -``` - -### Handling varying channel structures - -Channels with different numbers of elements (e.g. `[meta, bam]` vs `[meta, bam, bai]`) -are handled safely by always wrapping the entire inner tuple as a single second element. -Nextflow recursively scans the value for file objects automatically. - -// CORRECT -.map { meta, bam, bai -> ['alignment/', [meta, bam, bai]] } - -// WRONG — breaks the [destination, value] contract -.map { meta, bam, bai -> ['alignment/', meta, bam, bai] } -``` - -**Your command** — add one line to enforce the wrapping rule: -``` -... - -For each process output that should be published, map it into a tuple of -[destination_path, channel_value] where destination_path mirrors the directory -that publishDir was publishing to. Always wrap the entire channel value as a -single second element regardless of how many elements it contains, e.g. -{ meta, bam, bai -> ['alignment/', [meta, bam, bai]] }. -... - -### Grouping channels by destination before mapping - -Instead of mapping each channel individually, group channels sharing the same destination -using `mix` first, then apply a single `map` per destination group. This reduces repetition -significantly. - -```nextflow -// PREFERRED — one map per destination group -ch_qc_bam = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) - .mix(TIDDIT_COV.out.wig) - .mix(MOSDEPTH.out.global_txt) - .mix(ch_qualimap) - .map { meta, value -> ['qc_bam/', [meta, value]] } - -ch_ngsbits = ch_ngsbits_samplegender - .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] } - -ch_publish = ch_qc_bam.mix(ch_ngsbits) - -// AVOID — one map per channel, very repetitive -ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - .map { meta, metrics -> ['qc_bam/', [meta, metrics]] } - .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf - .map { meta, pdf -> ['qc_bam/', [meta, pdf]] }) - // ... -``` - -Rules: - -- Create one intermediate channel per unique destination directory -- Mix all channels going to the same destination first, then apply a single `map` -- Combine all destination groups into `ch_publish` with a final `mix` - -### Nested subworkflows — bubbling up ch_publish - -When a subworkflow calls other subworkflows, always mix the inner `ch_publish` into the -outer `ch_publish`. This propagates publishing up the call chain to `main.nf`. - -```nextflow -// Inner subworkflow emits its own ch_publish -workflow ALIGN_BWA { - main: - BWA_MEM(...) - SAMTOOLS_SORT(...) - - ch_publish = BWA_MEM.out.bam - .mix(SAMTOOLS_SORT.out.bam) - .map { meta, value -> ['alignment/', [meta, value]] } - - emit: - ch_publish -} - -// Outer subworkflow mixes in ch_publish from inner subworkflow -workflow ALIGN { - main: - ALIGN_BWA(...) - FASTP(...) - - ch_publish = FASTP.out.reads - .map { meta, value -> ['fastp/', [meta, value]] } - .mix(ALIGN_BWA.out.ch_publish) - - emit: - ch_publish -} -``` - -Rules: - -- Every subworkflow that has publishable outputs must emit `ch_publish` -- If a subworkflow calls inner subworkflows, always mix their `ch_publish` into the - outer `ch_publish` — never discard it -- In `main.nf`, mix `ch_publish` from all top-level subworkflows into one channel - before the `publish:` block - -### Why this approach - -- Subworkflow signatures stay clean — one `ch_publish` emit regardless of how many - output directories exist internally -- Publishing logic is fully centralized in `main.nf` -- No `topic` channel footguns (pipeline hanging forever if a process consumes its own topic) -- Easy to audit all published paths by reading `main.nf` alone diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 06df3a019..6efa84853 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -116,7 +116,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -217,7 +219,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -310,7 +314,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 93aa1301f..db6a471d1 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,369 +2,27 @@ "align bwamem2 - 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"timestamp": "2026-03-13T09:08:54.679899252", + "timestamp": "2026-03-13T12:50:51.679790362", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -612,132 +270,12 @@ "align bwameme - wgs": { "content": [ [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "slowlycivilbuck_sort_md.cram:md5,ef724cfbe1fc7c705f6d1c8098fa43dd" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "slowlycivilbuck_sort_md.cram.crai:md5,b5a31e143eb727a0a8296992ff5a13ba" - 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] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "slowlycivilbuck_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "slowlycivilbuck_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - [ - "hugelymodelbat_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "hugelymodelbat_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "trimming/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "hugelymodelbat.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "hugelymodelbat.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "hugelymodelbat.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "earlycasualcaiman_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "earlycasualcaiman_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "trimming/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + "earlycasualcaiman_sorted_md.bam", + "earlycasualcaiman_sorted_md.metrics.txt", + "hugelymodelbat_sorted_md.bam", + "hugelymodelbat_sorted_md.metrics.txt", + "slowlycivilbuck_sorted_md.bam", + "slowlycivilbuck_sorted_md.metrics.txt", + "earlycasualcaiman_sorted_md.bam.bai", + "hugelymodelbat_sorted_md.bam.bai", + "slowlycivilbuck_sorted_md.bam.bai", + "slowlycivilbuck_R1.fastp.fastq.gz", + "slowlycivilbuck_R2.fastp.fastq.gz", + "slowlycivilbuck.fastp.log", + "slowlycivilbuck.fastp.html", + "slowlycivilbuck.fastp.json", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", + "hugelymodelbat.fastp.log", + "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.html", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.html" ], [ [ @@ -1366,7 +502,7 @@ ] ], - "timestamp": "2026-03-13T09:09:46.038355114", + "timestamp": "2026-03-13T12:51:28.25179825", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 13fdcdf2a..b0cd92149 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -55,7 +55,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -112,7 +114,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index c61fe2bb9..523ca0a8b 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -2,54 +2,9 @@ "align bwamem2": { "content": [ [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,171423ac03499a00c4677f8b53771570" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,4730bcc5e26e8f3c29b8fa58f68d43e6" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,b8976cf366140eeee478ee2e9c1cadc9" - ] - ] + "test_sorted_md.bam", + "test_sorted_md.metrics.txt", + "test_sorted_md.bam.bai" ], [ [ @@ -82,7 +37,7 @@ ] ] ], - "timestamp": "2026-03-13T09:21:28.631120006", + "timestamp": "2026-03-13T13:02:30.573936764", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -91,54 +46,9 @@ "align bwameme": { "content": [ [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,ca247f01365899e07c77c3479fa721b2" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,f5b5580ca2b1035f0cac8ba1db7ab55e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,e1e422e8da8ae8f2fbf0221d29919be0" - ] - ] + "test_sorted_md.bam", + "test_sorted_md.metrics.txt", + "test_sorted_md.bam.bai" ], [ [ @@ -171,7 +81,7 @@ ] ] ], - "timestamp": "2026-03-13T09:22:14.004999114", + "timestamp": "2026-03-13T13:03:18.075557991", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 8664d596f..049378ff5 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -30,7 +30,9 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index a69390d12..ecfabe8f8 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -2,68 +2,14 @@ "CALL_REPEAT_EXPANSIONS": { "content": [ [ - [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_repeat_expansion.vcf:md5,9e2d2ec1df32e12dc2e043f7f5dae61c" - ] - ], - [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam:md5,32e22328efec8cdd3c818e18568f2108" - ] - ], - [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam.bai:md5,7cdcf4e866373d4aa0e762acfe0f5d5a" - ] - ] + "earlycasualcaiman_repeat_expansion.vcf", + "earlycasualcaiman_exphunter_sorted.bam", + "earlycasualcaiman_exphunter_sorted.bam.bai" ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-13T09:28:35.853691152", + "timestamp": "2026-03-13T12:38:25.736225141", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 727903fdf..87a4fca98 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -59,7 +59,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index c8a7b4c10..6639eb9bb 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -2,42 +2,10 @@ "CALL_SNV - deepvariant wgs": { "content": [ [ - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,b78d7a388ac51028ca8b15474b9efce6" - ] - ], - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,81c8e362552865ccdd12941db07bdf6e" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,5b31cdd1aaca1b52aa06ec49b0d3207f" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,057840edb22fe608c7635911a914e9f0" - ] - ] + "justhusky_snv.vcf.gz.tbi", + "justhusky_snv.vcf.gz", + "justhusky_mitochondria.vcf.gz", + "justhusky_mitochondria.vcf.gz.tbi" ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", @@ -48,7 +16,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-13T09:33:27.081509863", + "timestamp": "2026-03-13T13:11:10.952443789", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 26b2f362b..614370b8c 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -46,7 +46,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 999d3184e..f73f465ab 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -2,24 +2,8 @@ "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ [ - [ - "call_sv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_sv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + "justhusky_sv.vcf.gz", + "justhusky_sv.vcf.gz.tbi" ], [ "justhusky_sv.vcf.gz" @@ -28,7 +12,7 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-13T09:44:18.163494369", + "timestamp": "2026-03-13T13:21:51.525587168", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index f354e408c..edae66f98 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -54,7 +54,9 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.multiple_metrics .collect {it[1]} .flatten() @@ -133,7 +135,9 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.multiple_metrics .collect {it[1]} .flatten() diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index aa697e3ef..5ecb26245 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -81,77 +81,28 @@ "QC_BAM - test, sentieon": { "content": [ [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], [ ], [ - "earlycasualcaiman_wgsmetrics.txt" + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" - ] + ] ], - "timestamp": "2026-02-17T15:21:49.953972761", + "timestamp": "2026-03-12T23:44:03.5837213", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 88ad0489913a8d0f27513b5beffca441f6cbd281 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 14:17:15 +0100 Subject: [PATCH 06/19] update sentieon tests --- .../align_sentieon/tests/main.nf.test.snap | 10 +- .../local/qc_bam/tests/main.nf.test.snap | 777 ++++-------------- 2 files changed, 145 insertions(+), 642 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 9b1ad860b..b35de4106 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -200,7 +200,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -371,7 +371,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -387,7 +387,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -408,7 +408,7 @@ ] } ], - "timestamp": "2026-03-13T11:07:38.099732631", + "timestamp": "2026-03-13T14:06:49.285440618", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 22a3bd5b9..fd4bbf5e2 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,319 +2,50 @@ "QC_BAM - 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+ "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ ], [ - + "earlycasualcaiman_wgsmetrics.txt" ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] ] ], -<<<<<<< HEAD - "timestamp": "2026-03-12T23:44:03.5837213", -======= - "timestamp": "2026-03-13T11:15:12.139419029", ->>>>>>> aa5f8761cf1eb799367f2a31782c837c67345fbc + "timestamp": "2026-03-13T14:13:47.258652619", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 53557f314f15dab5e8879fd355081e688ce32843 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 14:37:07 +0100 Subject: [PATCH 07/19] add sort [skip ci] --- subworkflows/local/align/tests/main.nf.test | 9 ++++++--- .../local/align_bwa_bwamem2_bwameme/tests/main.nf.test | 6 ++++-- .../local/call_repeat_expansions/tests/main.nf.test | 3 ++- subworkflows/local/call_snv/tests/main.nf.test | 3 ++- .../local/call_structural_variants/tests/main.nf.test | 3 ++- subworkflows/local/qc_bam/tests/main.nf.test | 6 ++++-- 6 files changed, 20 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 6efa84853..410ea08d7 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -118,7 +118,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -221,7 +222,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -316,7 +318,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index b0cd92149..f45609486 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -57,7 +57,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -116,7 +117,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 049378ff5..c21805209 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -32,7 +32,8 @@ nextflow_workflow { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 87a4fca98..0d9fefce5 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -61,7 +61,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 614370b8c..94e520bcd 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -48,7 +48,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index edae66f98..79bbaaedc 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -56,7 +56,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.multiple_metrics .collect {it[1]} .flatten() @@ -137,7 +138,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.multiple_metrics .collect {it[1]} .flatten() From 221eee3669f49cc7ae5b6926e0587127b3924383 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 15:40:32 +0100 Subject: [PATCH 08/19] update sentieon snapshots [skip ci] --- .../align_sentieon/tests/main.nf.test.snap | 10 +-- .../local/qc_bam/tests/main.nf.test.snap | 64 +++++++++---------- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b35de4106..acbf733be 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ], [ @@ -200,7 +200,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ] ], @@ -371,7 +371,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ], [ @@ -387,7 +387,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ] ], @@ -408,7 +408,7 @@ ] } ], - "timestamp": "2026-03-13T14:06:49.285440618", + "timestamp": "2026-03-13T15:03:01.128235963", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index fd4bbf5e2..dcacf5eaf 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,12 +2,24 @@ "QC_BAM - test, bwamem2": { "content": [ [ - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_mosdepth.mosdepth.summary.txt", "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_qualimap", "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", "earlycasualcaiman_tidditcov_1.png", "earlycasualcaiman_tidditcov_10.png", "earlycasualcaiman_tidditcov_11.png", @@ -33,18 +45,6 @@ "earlycasualcaiman_tidditcov_M.png", "earlycasualcaiman_tidditcov_X.png", "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_qualimap", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" ], [ @@ -118,7 +118,7 @@ ] ] ], - "timestamp": "2026-03-13T14:12:57.09777024", + "timestamp": "2026-03-13T15:34:21.197802663", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -127,13 +127,24 @@ "QC_BAM - test, sentieon": { "content": [ [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", "earlycasualcaiman_mosdepth.mosdepth.summary.txt", "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_qualimap", "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_wgsmetrics.txt", + "earlycasualcaiman_tidditcov.wig", "earlycasualcaiman_tidditcov_1.png", "earlycasualcaiman_tidditcov_10.png", "earlycasualcaiman_tidditcov_11.png", @@ -159,18 +170,7 @@ "earlycasualcaiman_tidditcov_M.png", "earlycasualcaiman_tidditcov_X.png", "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_qualimap", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + "earlycasualcaiman_wgsmetrics.txt" ], [ "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", @@ -243,7 +243,7 @@ ] ] ], - "timestamp": "2026-03-13T14:13:47.258652619", + "timestamp": "2026-03-13T15:35:09.991615599", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 78bfd88df4d62d88800fd0af2f57e76e862a8c94 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 16:06:45 +0100 Subject: [PATCH 09/19] Update other snaps --- .../local/align/tests/main.nf.test.snap | 78 +++++++++---------- .../tests/main.nf.test.snap | 12 +-- .../tests/main.nf.test.snap | 6 +- .../local/call_snv/tests/main.nf.test.snap | 18 ++--- 4 files changed, 57 insertions(+), 57 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index db6a471d1..d1d0c7003 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,27 +2,27 @@ "align bwamem2 - wgs": { "content": [ [ - "slowlycivilbuck_sort_md.cram", - "slowlycivilbuck_sort_md.cram.crai", - "hugelymodelbat_sort_md.cram", - "hugelymodelbat_sort_md.cram.crai", + "earlycasualcaiman.fastp.html", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", "earlycasualcaiman_sort_md.cram", "earlycasualcaiman_sort_md.cram.crai", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat.fastp.log", "hugelymodelbat.fastp.html", "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.log", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", + "hugelymodelbat_sort_md.cram", + "hugelymodelbat_sort_md.cram.crai", + "slowlycivilbuck.fastp.html", + "slowlycivilbuck.fastp.json", + "slowlycivilbuck.fastp.log", "slowlycivilbuck_R1.fastp.fastq.gz", "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.html", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.html" + "slowlycivilbuck_sort_md.cram", + "slowlycivilbuck_sort_md.cram.crai" ], [ [ @@ -261,7 +261,7 @@ ] ] ], - "timestamp": "2026-03-13T12:50:51.679790362", + "timestamp": "2026-03-13T14:53:02.154281647", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -270,12 +270,12 @@ "align bwameme - wgs": { "content": [ [ + "earlycasualcaiman_sort_md.cram", + "earlycasualcaiman_sort_md.cram.crai", "hugelymodelbat_sort_md.cram", "hugelymodelbat_sort_md.cram.crai", "slowlycivilbuck_sort_md.cram", - "slowlycivilbuck_sort_md.cram.crai", - "earlycasualcaiman_sort_md.cram", - "earlycasualcaiman_sort_md.cram.crai" + "slowlycivilbuck_sort_md.cram.crai" ], [ [ @@ -399,7 +399,7 @@ ] ], - "timestamp": "2026-03-13T12:57:17.001367202", + "timestamp": "2026-03-13T14:59:34.430725854", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -408,30 +408,30 @@ "align bwamem2 - wes": { "content": [ [ + "earlycasualcaiman.fastp.html", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", "earlycasualcaiman_sorted_md.bam", + "earlycasualcaiman_sorted_md.bam.bai", "earlycasualcaiman_sorted_md.metrics.txt", + "hugelymodelbat.fastp.html", + "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.log", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", "hugelymodelbat_sorted_md.bam", - "hugelymodelbat_sorted_md.metrics.txt", - "slowlycivilbuck_sorted_md.bam", - "slowlycivilbuck_sorted_md.metrics.txt", - "earlycasualcaiman_sorted_md.bam.bai", "hugelymodelbat_sorted_md.bam.bai", - "slowlycivilbuck_sorted_md.bam.bai", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck.fastp.log", + "hugelymodelbat_sorted_md.metrics.txt", "slowlycivilbuck.fastp.html", "slowlycivilbuck.fastp.json", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat.fastp.log", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.html", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.html" + "slowlycivilbuck.fastp.log", + "slowlycivilbuck_R1.fastp.fastq.gz", + "slowlycivilbuck_R2.fastp.fastq.gz", + "slowlycivilbuck_sorted_md.bam", + "slowlycivilbuck_sorted_md.bam.bai", + "slowlycivilbuck_sorted_md.metrics.txt" ], [ [ @@ -502,7 +502,7 @@ ] ], - "timestamp": "2026-03-13T12:51:28.25179825", + "timestamp": "2026-03-13T14:53:37.576915277", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 523ca0a8b..7632f79b8 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -3,8 +3,8 @@ "content": [ [ "test_sorted_md.bam", - "test_sorted_md.metrics.txt", - "test_sorted_md.bam.bai" + "test_sorted_md.bam.bai", + "test_sorted_md.metrics.txt" ], [ [ @@ -37,7 +37,7 @@ ] ] ], - "timestamp": "2026-03-13T13:02:30.573936764", + "timestamp": "2026-03-13T15:04:33.885203481", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -47,8 +47,8 @@ "content": [ [ "test_sorted_md.bam", - "test_sorted_md.metrics.txt", - "test_sorted_md.bam.bai" + "test_sorted_md.bam.bai", + "test_sorted_md.metrics.txt" ], [ [ @@ -81,7 +81,7 @@ ] ] ], - "timestamp": "2026-03-13T13:03:18.075557991", + "timestamp": "2026-03-13T15:05:20.75721248", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index ecfabe8f8..58e9e8bd7 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "CALL_REPEAT_EXPANSIONS": { "content": [ [ - "earlycasualcaiman_repeat_expansion.vcf", "earlycasualcaiman_exphunter_sorted.bam", - "earlycasualcaiman_exphunter_sorted.bam.bai" + "earlycasualcaiman_exphunter_sorted.bam.bai", + "earlycasualcaiman_repeat_expansion.vcf" ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-13T12:38:25.736225141", + "timestamp": "2026-03-13T15:42:01.510910485", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 6639eb9bb..da2926ecf 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -2,10 +2,10 @@ "CALL_SNV - deepvariant wgs": { "content": [ [ - "justhusky_snv.vcf.gz.tbi", - "justhusky_snv.vcf.gz", "justhusky_mitochondria.vcf.gz", - "justhusky_mitochondria.vcf.gz.tbi" + "justhusky_mitochondria.vcf.gz.tbi", + "justhusky_snv.vcf.gz", + "justhusky_snv.vcf.gz.tbi" ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", @@ -16,7 +16,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-13T13:11:10.952443789", + "timestamp": "2026-03-13T15:46:57.105465403", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -109,7 +109,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -118,7 +118,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -224,7 +224,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -233,7 +233,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -257,7 +257,7 @@ ] } ], - "timestamp": "2026-03-13T09:34:33.930010907", + "timestamp": "2026-03-13T15:48:00.031080535", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 736592df715f4515b6a1ada0583aad527fdfd60d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 17:20:29 +0100 Subject: [PATCH 10/19] update nxf version --- .github/workflows/nf-test.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 6b7dade1f..a36628850 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -77,7 +77,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.04.0" + - "25.10.4" - "latest-everything" env: NXF_ANSI_LOG: false diff --git a/nextflow.config b/nextflow.config index 4c212227e..47745af8d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -464,7 +464,7 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=25.04.0' + nextflowVersion = '!>=25.10.4' version = '2.7.0dev' doi = '10.5281/zenodo.7995798' } From 746ba255b735e460ab4a3b336bd7d1c7cdf1f5c2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:11:22 +0000 Subject: [PATCH 11/19] update snap for postprocess MT [skip ci] --- subworkflows/local/postprocess_MT_calls/main.nf | 6 +++--- .../local/postprocess_MT_calls/tests/main.nf.test.snap | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index ef10982ec..a9ecdf01b 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -125,7 +125,7 @@ workflow POSTPROCESS_MT_CALLS { .map { meta, value -> ['call_snv/mitochondria/', [meta, value]] } emit: - tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap index fa37649d4..6ddd843ef 100644 --- a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap @@ -38,7 +38,7 @@ ] ] ], - "ch_publish": [ + "publish": [ [ "call_snv/mitochondria/", [ @@ -76,7 +76,7 @@ ] } ], - "timestamp": "2026-03-12T23:41:04.472222425", + "timestamp": "2026-03-13T22:07:26.775535698", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 0b74fb3db869c878b79b98136752902e2f335c68 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 23:22:56 +0100 Subject: [PATCH 12/19] update sentieon snapshot --- .../local/align_sentieon/tests/main.nf.test.snap | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index acbf733be..2fcbd8e27 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -200,7 +200,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -371,7 +371,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -387,7 +387,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -408,7 +408,7 @@ ] } ], - "timestamp": "2026-03-13T15:03:01.128235963", + "timestamp": "2026-03-13T23:08:12.022075352", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From ef5ec40cc6d6fb00038d1084690bb5370bfdeda8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:33:52 +0000 Subject: [PATCH 13/19] Update ro-crate-metadata.json --- ro-crate-metadata.json | 65 ++++++++++++++++++++++++------------------ 1 file changed, 37 insertions(+), 28 deletions(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d16ffbb32..d2187ded7 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-08T12:27:15+00:00", + "datePublished": "2026-03-13T22:32:54+00:00", "description": "

\n \n \n \"nf-core/raredisease\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#1b26a4ae-2b56-4c74-8235-6a6320ec1067" + "@id": "#acbb265d-df95-4c8c-b241-9c704c07f759" } ], "name": "nf-core/raredisease" @@ -134,26 +134,29 @@ ], "creator": [ { - "@id": "https://orcid.org/0000-0002-2219-0197" + "@id": "https://orcid.org/0000-0003-1316-2845" }, { - "@id": "https://orcid.org/0000-0002-4100-9963" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { "@id": "https://orcid.org/0000-0002-5044-7754" }, { - "@id": "https://orcid.org/0000-0003-1316-2845" + "@id": "https://orcid.org/0009-0005-4189-8704" }, { "@id": "#25568561+projectoriented@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "https://orcid.org/0000-0002-2219-0197" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963" } ], "dateCreated": "", - "dateModified": "2025-07-08T14:27:15Z", + "dateModified": "2026-03-13T22:32:54Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,10 +175,7 @@ ], "maintainer": [ { - "@id": "https://orcid.org/0000-0002-2219-0197" - }, - { - "@id": "https://orcid.org/0000-0002-4100-9963" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { "@id": "https://orcid.org/0000-0002-5044-7754" @@ -184,7 +184,10 @@ "@id": "#25568561+projectoriented@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "https://orcid.org/0000-0002-2219-0197" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963" } ], "name": [ @@ -214,14 +217,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.04.0" + "version": "!>=25.10.4" }, { - "@id": "#1b26a4ae-2b56-4c74-8235-6a6320ec1067", + "@id": "#acbb265d-df95-4c8c-b241-9c704c07f759", "@type": "TestSuite", "instance": [ { - "@id": "#34b99e0d-03ba-4190-be8d-081702d44958" + "@id": "#e2389f87-0193-4a16-a8f1-7dab97ad2636" } ], "mainEntity": { @@ -230,7 +233,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#34b99e0d-03ba-4190-be8d-081702d44958", + "@id": "#e2389f87-0193-4a16-a8f1-7dab97ad2636", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -369,16 +372,16 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0000-0002-2219-0197", + "@id": "https://orcid.org/0000-0003-1316-2845", "@type": "Person", - "email": "jemten@users.noreply.github.com", - "name": "Anders Jemt" + "email": "raysloks@gmail.com", + "name": "Emil Bertilsson" }, { - "@id": "https://orcid.org/0000-0002-4100-9963", + "@id": "https://orcid.org/0000-0001-7313-3734", "@type": "Person", - "email": "Gwenna.breton@gu.se", - "name": "Gwenna Breton" + "email": "20065894+ramprasadn@users.noreply.github.com", + "name": "Ramprasad Neethiraj" }, { "@id": "https://orcid.org/0000-0002-5044-7754", @@ -387,10 +390,10 @@ "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" }, { - "@id": "https://orcid.org/0000-0003-1316-2845", + "@id": "https://orcid.org/0009-0005-4189-8704", "@type": "Person", - "email": "raysloks@gmail.com", - "name": "Emil Bertilsson" + "email": "75395041+ieduba@users.noreply.github.com", + "name": "Irene Duba" }, { "@id": "#25568561+projectoriented@users.noreply.github.com", @@ -399,10 +402,16 @@ "name": "Mei Wu" }, { - "@id": "https://orcid.org/0000-0001-7313-3734", + "@id": "https://orcid.org/0000-0002-2219-0197", "@type": "Person", - "email": "20065894+ramprasadn@users.noreply.github.com", - "name": "Ramprasad Neethiraj" + "email": "jemten@users.noreply.github.com", + "name": "Anders Jemt" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963", + "@type": "Person", + "email": "Gwenna.breton@gu.se", + "name": "Gwenna Breton" } ] } \ No newline at end of file From 21dc6957ab298eaad0116d37cb1efbfae905088c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:34:21 +0000 Subject: [PATCH 14/19] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ca86e4e5d..6a6abb6d0 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) From 4a3734c5718e45b075abfbcfcce2753f29bd9124 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:41:37 +0000 Subject: [PATCH 15/19] Update nf-test.yml --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index a36628850..1009d5eea 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -50,7 +50,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 14 + max_shards: 20 - name: debug run: | From 6c7ba9b2805deb29d5f65ec536d62a24dacceeb4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 14 Mar 2026 00:04:03 +0100 Subject: [PATCH 16/19] update sentieon snapshot --- .../local/align_sentieon/tests/main.nf.test | 15 +- .../align_sentieon/tests/main.nf.test.snap | 533 +++++------------- 2 files changed, 141 insertions(+), 407 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 9c36901c8..4954858c8 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -49,7 +49,20 @@ nextflow_workflow { then { assert workflow.success - assert snapshot(workflow.out).match() + assert snapshot( + workflow.out.marked_bam, + workflow.out.marked_bai, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort(), + ).match() } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 2fcbd8e27..b538612cb 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -1,414 +1,135 @@ { "align sentieon": { "content": [ - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" - ] - ], - "6": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" - ] - ], - "7": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" - ] - ], - "8": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ] - ], - "aln_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" - ] - ], - "gc_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" - ] - ], - "gc_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" - ] - ], - "is_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" - ] - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - "mq_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ] - ], - "qd_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" - ] + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] - } + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" + ] + ], + [ + "test_dedup.bam", + "test_dedup.bam.bai", + "test_dedup.bam.metrics", + "test_dedup.bam.metrics.multiqc.tsv", + "test_dedup.score" + ] ], - "timestamp": "2026-03-13T23:08:12.022075352", + "timestamp": "2026-03-14T00:02:24.597092362", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 1de736c2a57cc5c009bef039e1323b6610e0ba7a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 14:42:24 +0100 Subject: [PATCH 17/19] Migrate strange and subsampling workflows to output and update snapshot --- conf/modules/raredisease.config | 5 ----- conf/modules/subsample_mt_frac.config | 5 ----- conf/modules/subsample_mt_reads.config | 5 ----- subworkflows/local/subsample_mt_frac/main.nf | 6 ++++++ subworkflows/local/subsample_mt_reads/main.nf | 6 ++++++ tests/default.nf.test.snap | 12 +----------- tests/test_bam.nf.test.snap | 12 +----------- tests/test_singleton.nf.test.snap | 8 +------- workflows/raredisease.nf | 8 ++++++++ 9 files changed, 23 insertions(+), 44 deletions(-) diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config index 0b01c4488..111949302 100644 --- a/conf/modules/raredisease.config +++ b/conf/modules/raredisease.config @@ -65,11 +65,6 @@ process { process { withName: '.*STRANGER' { ext.prefix = { "${meta.id}_repeat_expansion_stranger" } - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } } diff --git a/conf/modules/subsample_mt_frac.config b/conf/modules/subsample_mt_frac.config index 5b3e6e17c..32ba66748 100644 --- a/conf/modules/subsample_mt_frac.config +++ b/conf/modules/subsample_mt_frac.config @@ -24,11 +24,6 @@ process { withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_VIEW' { ext.args = { "--output-fmt BAM -h -F 4 -s ${meta.seedfrac}" } ext.prefix = { "${meta.id}_mt_subsample" } - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/subsample_mt_reads.config b/conf/modules/subsample_mt_reads.config index 70f9a71ef..d8525b521 100644 --- a/conf/modules/subsample_mt_reads.config +++ b/conf/modules/subsample_mt_reads.config @@ -40,11 +40,6 @@ process { withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_SORT' { ext.prefix = { "${meta.id}_mt_subsample" } - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 6ac7c6c98..1ea24dac0 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -32,4 +32,10 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[],[]], [], 'bai') + ch_publish = SAMTOOLS_VIEW.out.bam + .mix(SAMTOOLS_VIEW.out.bai) + .map { meta, value -> ['alignment/', [meta, value]] } + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index e141eaea3..3f75a74d4 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -26,4 +26,10 @@ workflow SUBSAMPLE_MT_READS { SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') + ch_publish = SAMTOOLS_SORT.out.bam + .mix(SAMTOOLS_SORT.out.bai) + .map { meta, value -> ['alignment/', [meta, value]] } + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 538aa9fcc..5652128ce 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -499,13 +499,6 @@ } }, [ - "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/hugelymodelbat_mt_subsample.bam", - "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -703,9 +696,6 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -716,7 +706,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-12T22:37:05.921453831", + "timestamp": "2026-03-16T14:20:06.249313916", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9c508f269..07be8aab3 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -469,13 +469,6 @@ } }, [ - "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/hugelymodelbat_mt_subsample.bam", - "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -663,9 +656,6 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -676,7 +666,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-12T22:43:18.380887473", + "timestamp": "2026-03-16T14:26:16.566396016", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index f23ae4108..e970226a5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -482,9 +482,6 @@ } }, [ - "alignment", - "alignment/hugelymodelbat_mt_subsample.bam", - "alignment/hugelymodelbat_mt_subsample.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -568,9 +565,6 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -579,7 +573,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-12T22:47:05.119730547", + "timestamp": "2026-03-16T14:30:06.728297714", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8d78db201..0dc5c7385 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -213,6 +213,7 @@ workflow RAREDISEASE { ch_call_sv_mt_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() + ch_subsample_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -289,10 +290,12 @@ workflow RAREDISEASE { val_mt_subsample_rd, val_mt_subsample_seed ) + ch_subsample_publish = SUBSAMPLE_MT_FRAC.out.publish } else { SUBSAMPLE_MT_READS( ch_mapped.mt_bam_bai, ) + ch_subsample_publish = SUBSAMPLE_MT_READS.out.publish } } @@ -353,6 +356,10 @@ workflow RAREDISEASE { CALL_REPEAT_EXPANSIONS.out.vcf, ch_variant_catalog ) + ch_call_repeat_expansions_publish = ch_call_repeat_expansions_publish + .mix(STRANGER.out.vcf + .mix(STRANGER.out.tbi) + .map { meta, value -> ['repeat_expansions/', [meta, value]] }) } } @@ -910,6 +917,7 @@ workflow RAREDISEASE { versions = ch_versions // channel: [ path(versions.yml) ] publish = ch_align_publish .mix(ch_qc_bam_publish) + .mix(ch_subsample_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) .mix(ch_call_sv_mt_publish) From 2659d9797691124127b9120caa0324968c79cb1b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 14:43:33 +0100 Subject: [PATCH 18/19] Update nextflow.config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 4c212227e..4c6e7d0c0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -175,6 +175,7 @@ params { validate_params = true } +outputDir = params.outdir workflow.output.mode = 'copy' // Load base.config by default for all pipelines From 6b5625adba45341370e63bad3afbd0d8696a6726 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 18:28:04 +0100 Subject: [PATCH 19/19] update snapshot --- tests/default.nf.test.snap | 396 +++++++++++++++++++++++++++++- tests/test_bam.nf.test.snap | 365 ++++++++++++++++++++++++++- tests/test_singleton.nf.test.snap | 148 ++++++++++- 3 files changed, 906 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5652128ce..ddbbe0fb6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -499,6 +499,22 @@ } }, [ + "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", + "alignment/earlycasualcaiman_sorted_md.metrics.txt", + "alignment/hugelymodelbat_mt_subsample.bam", + "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", + "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -653,6 +669,30 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", + "call_snv", + "call_snv/genome", + "call_snv/genome/justhusky_snv.vcf.gz", + "call_snv/genome/justhusky_snv.vcf.gz.tbi", + "call_snv/mitochondria", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", + "call_sv", + "call_sv/genome", + "call_sv/genome/justhusky_sv.vcf.gz", + "call_sv/genome/justhusky_sv.vcf.gz.tbi", + "call_sv/mitochondria", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", + 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"qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", + "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -656,6 +1007,18 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", + "repeat_expansions", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", + "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", + "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -666,7 +1029,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-16T14:26:16.566396016", + "timestamp": "2026-03-16T18:18:03.478560166", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e970226a5..e597eca33 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -482,6 +482,12 @@ } }, [ + "alignment", + "alignment/hugelymodelbat_mt_subsample.bam", + "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -528,6 +534,24 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", + "call_snv", + "call_snv/genome", + "call_snv/genome/justhusky_snv.vcf.gz", + "call_snv/genome/justhusky_snv.vcf.gz.tbi", + "call_snv/mitochondria", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", + "call_sv", + "call_sv/genome", + "call_sv/genome/justhusky_sv.vcf.gz", + "call_sv/genome/justhusky_sv.vcf.gz.tbi", + "call_sv/mitochondria", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", + "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -537,6 +561,8 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", + "ngsbits_samplegender", + "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -552,6 +578,114 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", + "qc_bam", + "qc_bam/hugelymodelbat", + "qc_bam/hugelymodelbat/css", + "qc_bam/hugelymodelbat/css/agogo.css", + "qc_bam/hugelymodelbat/css/ajax-loader.gif", + 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