From 5a86d2a4a7ce1c12cee5e6b01915c0fd1091fd65 Mon Sep 17 00:00:00 2001 From: DogaTestere Date: Fri, 13 Mar 2026 16:36:08 +0300 Subject: [PATCH] Migrate dragen/germline module to topic channels --- modules/nf-core/dragen/germline/main.nf | 12 +- modules/nf-core/dragen/germline/meta.yml | 245 ++++++++++++++++-- .../dragen/germline/tests/main.nf.test | 2 +- .../dragen/germline/tests/main.nf.test.snap | 48 ++-- 4 files changed, 247 insertions(+), 60 deletions(-) diff --git a/modules/nf-core/dragen/germline/main.nf b/modules/nf-core/dragen/germline/main.nf index 9dca21580ef4..8761e24a0839 100644 --- a/modules/nf-core/dragen/germline/main.nf +++ b/modules/nf-core/dragen/germline/main.nf @@ -188,7 +188,7 @@ process DRAGEN { path "streaming_log_*.csv" , optional: true, emit: streaming_log_csv path "*_usage.txt" , emit: usage_txt path "**" , emit: all - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('dragen'), eval("dragen --version 2>&1 | sed 's/^dragen Version //;s/ Hash.*//'"), emit: versions_dragen, topic: versions when: task.ext.when == null || task.ext.when @@ -394,11 +394,6 @@ process DRAGEN { $format_input \\ --output-file-prefix $prefix \\ --output-directory \$(pwd) - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - dragen: \$(echo \$(dragen --version 2>&1) | sed 's/^dragen Version //;s/ Hash.*//') - END_VERSIONS """ stub: @@ -406,10 +401,5 @@ process DRAGEN { prefix = task.ext.prefix ?: "${meta.id}" """ touch 20251120_usage.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - dragen: ${VERSION} - END_VERSIONS """ } diff --git a/modules/nf-core/dragen/germline/meta.yml b/modules/nf-core/dragen/germline/meta.yml index 6ec34e715d0c..c39fe67417c8 100644 --- a/modules/nf-core/dragen/germline/meta.yml +++ b/modules/nf-core/dragen/germline/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "dragen" description: The DRAGEN DNA Germline Pipeline accelerates the secondary analysis of NGS data by harnessing the tremendous power available on the DRAGEN @@ -43,7 +42,7 @@ input: description: FASTQ (may be gzipped), ora, BAM or CRAM files pattern: "*.{fastq,fq,ora,bam,cram}{,.gz}" ontologies: - - edam: http://edamontology.org/format_1930 # FASTQ + - edam: http://edamontology.org/format_1930 - checkfingerprint_expected_vcf: type: file description: Input expected genotypes (VCF) for checkfingerprint comparison @@ -54,7 +53,7 @@ input: description: Specify combined PON file pattern: "*.combined.counts.txt.gz" ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 - cnv_exclude_bed: type: file description: Regions to exclude for CNV processing @@ -249,8 +248,11 @@ output: e.g. `[ id:'sample1', single_end:false, sex:'female' ]` - ${prefix}-replay.json: type: file - description: Contains the exact set of parameters that specifies the analysis + description: Contains the exact set of parameters that specifies the + analysis pattern: "*-replay.json" + ontologies: + - edam: http://edamontology.org/format_3464 coverage_metrics_csv: - - meta: type: map @@ -259,8 +261,11 @@ output: e.g. `[ id:'sample1', single_end:false, sex:'female' ]` - ${prefix}.*_coverage_metrics.csv: type: file - description: Provides metrics over a region, a target region, or a QC coverage region + description: Provides metrics over a region, a target region, or a QC + coverage region pattern: "*.*_coverage_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 SJ_saturation_txt: - - meta: type: map @@ -271,6 +276,7 @@ output: type: file description: Measures sequencing saturation of the library pattern: "*.SJ.saturation.txt" + ontologies: [] baf_bedgraph_gz: - - meta: type: map @@ -281,6 +287,8 @@ output: type: file description: Contains b-allele counting pattern: "*.baf.bedgraph.gz" + ontologies: + - edam: http://edamontology.org/format_3989 baf_bw: - - meta: type: map @@ -291,6 +299,7 @@ output: type: file description: BigWig file containing variants pattern: "*.baf.bw" + ontologies: [] baf_seg: - - meta: type: map @@ -301,6 +310,7 @@ output: type: file description: Contains segmentation of b-allele loci pattern: "*.baf.seg" + ontologies: [] baf_seq_bw: - - meta: type: map @@ -311,6 +321,7 @@ output: type: file description: BigWig representation of the BAF segments pattern: "*.baf.seq.bw" + ontologies: [] ballele_counts_gz: - - meta: type: map @@ -321,6 +332,8 @@ output: type: file description: TSV-file containing b-allele counts pattern: "*.ballele.counts.gz" + ontologies: + - edam: http://edamontology.org/format_3989 bam: - - meta: type: map @@ -331,6 +344,7 @@ output: type: file description: Contains aligned reads pattern: "*.bam" + ontologies: [] bam_bai: - - meta: type: map @@ -341,6 +355,7 @@ output: type: file description: Index file for the BAM file pattern: "*.bam.bai" + ontologies: [] bam_md5sum: - - meta: type: map @@ -351,6 +366,7 @@ output: type: file description: MD5 checksum file for the BAM file pattern: "*.bam.md5sum" + ontologies: [] cnv_excluded_intervals_bed_gz: - - meta: type: map @@ -361,6 +377,8 @@ output: type: file description: Contains excluded intervals from CNV analysis pattern: "*.cnv.excluded_intervals.bed.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_gff3: - - meta: type: map @@ -371,6 +389,7 @@ output: type: file description: GFF3 representation of the CNV events pattern: "*.cnv.gff3" + ontologies: [] cnv_igv_session_xml: - - meta: type: map @@ -381,6 +400,8 @@ output: type: file description: IGV session XML file is prepopulated with track files pattern: "*.cnv.igv_session.xml" + ontologies: + - edam: http://edamontology.org/format_2332 cnv_pon_correlation_txt_gz: - - meta: type: map @@ -391,6 +412,8 @@ output: type: file description: PON Correlation File pattern: "*.cnv.pon_correlation.txt.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_pon_metrics_tsv_gz: - - meta: type: map @@ -401,6 +424,8 @@ output: type: file description: PON Metrics File pattern: "*.cnv.pon_metrics.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_purity_coverage_models_tsv: - - meta: type: map @@ -409,8 +434,11 @@ output: e.g. `[ id:'sample1', single_end:false, sex:'female' ]` - ${prefix}.cnv.purity.coverage.models.tsv: type: file - description: Describes the different tested models and their log-likelihood + description: Describes the different tested models and their + log-likelihood pattern: "*.cnv.purity.coverage.models.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 cnv_segdups_joint_coverage_tsv_gz: - - meta: type: map @@ -421,6 +449,8 @@ output: type: file description: Contains normalized joint coverage pattern: "*.cnv.segdups.joint_coverage.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_segdups_rescued_intervals_tsv_gz: - - meta: type: map @@ -431,6 +461,8 @@ output: type: file description: Contains rescued intervals pattern: "*.cnv.segdups.rescued_intervals.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_segdups_site_ratios_tsv_gz: - - meta: type: map @@ -439,8 +471,11 @@ output: e.g. `[ id:'sample1', single_end:false, sex:'female' ]` - ${prefix}.cnv.segdups.site_ratios.tsv.gz: type: file - description: Contains proportion of coverage to associate to the first and to the second interval + description: Contains proportion of coverage to associate to the first + and to the second interval pattern: "*.cnv.segdups.site_ratios.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_vcf: - - meta: type: map @@ -451,6 +486,7 @@ output: type: file description: VCF file containing CNV variants pattern: "*.cnv.vcf" + ontologies: [] cnv_vcf_gz: - - meta: type: map @@ -461,6 +497,8 @@ output: type: file description: Gzipped VCF file containing CNV variants pattern: "*.cnv.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cnv_vcf_gz_md5sum: - - meta: type: map @@ -471,6 +509,7 @@ output: type: file description: MD5 checksum file for the gzipped CNV VCF pattern: "*.cnv.vcf.gz.md5sum" + ontologies: [] cnv_vcf_gz_tbi: - - meta: type: map @@ -481,6 +520,7 @@ output: type: file description: Index file for the gzipped CNV VCF pattern: "*.cnv.vcf.gz.tbi" + ontologies: [] cnv_metrics_csv: - - meta: type: map @@ -491,6 +531,8 @@ output: type: file description: Contains CNV metrics pattern: "*.cnv_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 cnv_sv_vcf_gz: - - meta: type: map @@ -501,6 +543,8 @@ output: type: file description: Gzipped VCF file containing CNV structural variants pattern: "*.cnv_sv.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 combined_counts_txt_gz: - - meta: type: map @@ -509,8 +553,11 @@ output: e.g. `[ id:'sample1', single_end:false, sex:'female' ]` - ${prefix}.combined.counts.txt.gz: type: file - description: Column-wise concatenation of individual counts used to form the panel of normals + description: Column-wise concatenation of individual counts used to form + the panel of normals pattern: "*.combined.counts.txt.gz" + ontologies: + - edam: http://edamontology.org/format_3989 cram: - - meta: type: map @@ -521,6 +568,7 @@ output: type: file description: Contains aligned reads in CRAM format pattern: "*.cram" + ontologies: [] cram_crai: - - meta: type: map @@ -531,6 +579,7 @@ output: type: file description: Index file for the CRAM file pattern: "*.cram.crai" + ontologies: [] cram_md5sum: - - meta: type: map @@ -541,6 +590,7 @@ output: type: file description: MD5 checksum file for the CRAM file pattern: "*.cram.md5sum" + ontologies: [] excluded_intervals_bed_gz: - - meta: type: map @@ -551,6 +601,8 @@ output: type: file description: Gzipped BED file containing excluded intervals pattern: "*.excluded_intervals.bed.gz" + ontologies: + - edam: http://edamontology.org/format_3989 fastqc_metrics_csv: - - meta: type: map @@ -561,6 +613,8 @@ output: type: file description: FastQC metrics file pattern: "*.fastqc_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 fragment_length_hist_csv: - - meta: type: map @@ -571,6 +625,8 @@ output: type: file description: Contains insert length distribution pattern: "*.fragment_length_hist.csv" + ontologies: + - edam: http://edamontology.org/format_3752 g_vcf_gz: - - meta: type: map @@ -581,6 +637,8 @@ output: type: file description: Gzipped VCF file containing genomic variants pattern: "*.g.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 g_vcf_gz_tbi: - - meta: type: map @@ -591,6 +649,7 @@ output: type: file description: Index file for the gzipped VCF pattern: "*.g.vcf.gz.tbi" + ontologies: [] gc_metrics_csv: - - meta: type: map @@ -601,6 +660,8 @@ output: type: file description: Contains GC content metrics pattern: "*.gc_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 hard_filtered_baf_bw: - - meta: type: map @@ -611,6 +672,7 @@ output: type: file description: BigWig file containing hard-filtered BAF segments pattern: "*.hard-filtered.baf.bw" + ontologies: [] hard_filtered_gvcf_gz_md5sum: - - meta: type: map @@ -621,6 +683,7 @@ output: type: file description: MD5 checksum file for the gzipped hard-filtered GVCF pattern: "*.hard-filtered.gvcf.gz.md5sum" + ontologies: [] hard_filtered_vcf: - - meta: type: map @@ -631,6 +694,7 @@ output: type: file description: VCF file containing hard-filtered variants pattern: "*.hard-filtered.vcf" + ontologies: [] hard_filtered_vcf_gz: - - meta: type: map @@ -641,6 +705,8 @@ output: type: file description: Gzipped VCF file containing hard-filtered variants pattern: "*.hard-filtered.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 hard_filtered_vcf_gz_md5sum: - - meta: type: map @@ -651,6 +717,7 @@ output: type: file description: MD5 checksum file for the gzipped hard-filtered VCF pattern: "*.hard-filtered.vcf.gz.md5sum" + ontologies: [] hard_filtered_vcf_gz_tbi: - - meta: type: map @@ -661,6 +728,7 @@ output: type: file description: Index file for the gzipped hard-filtered VCF pattern: "*.hard-filtered.vcf.gz.tbi" + ontologies: [] improper_pairs_bw: - - meta: type: map @@ -671,6 +739,7 @@ output: type: file description: BigWig file containing improper read pairs pattern: "*.improper.pairs.bw" + ontologies: [] impute_chunk_out_txt: - - meta: type: map @@ -679,8 +748,10 @@ output: e.g. `[ id:'sample1', single_end:false, sex:'female' ]` - ${prefix}.impute.chunk.out.txt: type: file - description: Contains chunk regions to be passed along to the internal phase step + description: Contains chunk regions to be passed along to the internal + phase step pattern: "*.impute.chunk.out.txt" + ontologies: [] impute_phase_out_txt: - - meta: type: map @@ -691,6 +762,7 @@ output: type: file description: List containing all VCF files pattern: "*.impute.phase.out.txt" + ontologies: [] impute_vcf_gz: - - meta: type: map @@ -701,6 +773,8 @@ output: type: file description: Gzipped VCF file containing imputed variants pattern: "*.impute.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 insert_stats_tab: - - meta: type: map @@ -711,6 +785,8 @@ output: type: file description: Contains insert size statistics pattern: "*.insert-stats.tab" + ontologies: + - edam: http://edamontology.org/format_3475 mapping_metrics_csv: - - meta: type: map @@ -721,6 +797,8 @@ output: type: file description: Contains mapping metrics pattern: "*.mapping_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 multiomics_barcodeSummary_tsv: - - meta: type: map @@ -731,6 +809,8 @@ output: type: file description: Contains barcode summary information pattern: "*.multiomics.barcodeSummary.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 multiomics_barcodes_tsv_gz: - - meta: type: map @@ -741,6 +821,8 @@ output: type: file description: Gzipped File containing barcode summary information pattern: "*.multiomics.barcodes.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 multiomics_features_tsv_gz: - - meta: type: map @@ -751,6 +833,8 @@ output: type: file description: Gzipped file containing multiomics features pattern: "*.multiomics.features.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 multiomics_filtered_barcodes_tsv_gz: - - meta: type: map @@ -761,6 +845,8 @@ output: type: file description: Gzipped file containing filtered barcode information pattern: "*.multiomics.filtered.barcodes.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 multiomics_matrix_mtx_gz: - - meta: type: map @@ -771,6 +857,8 @@ output: type: file description: Gzipped matrix file containing multiomics data pattern: "*.multiomics.matrix.mtx.gz" + ontologies: + - edam: http://edamontology.org/format_3989 multiomics_metrics_csv: - - meta: type: map @@ -781,6 +869,8 @@ output: type: file description: Contains multiomics metrics pattern: "*.multiomics.metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 pcr_model_log: - - meta: type: map @@ -791,6 +881,7 @@ output: type: file description: Log file containing PCR model information pattern: "*.pcr-mode*.log" + ontologies: [] ploidy_vcf: - - meta: type: map @@ -801,6 +892,7 @@ output: type: file description: Contains ploidy information in VCF format pattern: "*.ploidy.vcf" + ontologies: [] ploidy_vcf_gz: - - meta: type: map @@ -811,6 +903,8 @@ output: type: file description: Gzipped VCF file containing ploidy information pattern: "*.ploidy.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 ploidy_vcf_gz_md5sum: - - meta: type: map @@ -821,6 +915,7 @@ output: type: file description: MD5 checksum file for the gzipped ploidy VCF pattern: "*.ploidy.vcf.gz.md5sum" + ontologies: [] ploidy_vcf_gz_tbi: - - meta: type: map @@ -831,6 +926,7 @@ output: type: file description: Index file for the gzipped ploidy VCF pattern: "*.ploidy.vcf.gz.tbi" + ontologies: [] ploidy_estimation_metrics_csv: - - meta: type: map @@ -841,6 +937,8 @@ output: type: file description: Contains metrics related to ploidy estimation pattern: "*.ploidy_estimation_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 preprocess_vcf_gz: - - meta: type: map @@ -851,6 +949,8 @@ output: type: file description: Gzipped VCF file containing preprocessed variants pattern: "*.preprocess.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 quant_genes_sf: - - meta: type: map @@ -861,6 +961,7 @@ output: type: file description: Contains gene quantification results in Salmon format pattern: "*.quant.genes.sf" + ontologies: [] quant_metrics_csv: - - meta: type: map @@ -871,6 +972,8 @@ output: type: file description: Contains quantification metrics in CSV format pattern: "*.quant.metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 quant_sf: - - meta: type: map @@ -881,6 +984,7 @@ output: type: file description: Contains quantification results in Salmon format pattern: "*.quant.sf" + ontologies: [] quant_transcript_coverage_txt: - - meta: type: map @@ -891,6 +995,7 @@ output: type: file description: Contains transcript coverage information pattern: "*.quant.transcript_coverage.txt" + ontologies: [] quant_transcript_fragment_lengths_txt: - - meta: type: map @@ -901,6 +1006,7 @@ output: type: file description: Contains transcript fragment lengths pattern: "*.quant.transcript_fragment_lengths.txt" + ontologies: [] realigned_regions_bed: - - meta: type: map @@ -911,6 +1017,7 @@ output: type: file description: Contains regions that have been realigned pattern: "*.realigned-regions.bed" + ontologies: [] repeats_bam: - - meta: type: map @@ -921,6 +1028,7 @@ output: type: file description: Contains reads aligned to repeat regions pattern: "*.repeats.bam" + ontologies: [] repeats_vcf: - - meta: type: map @@ -931,6 +1039,7 @@ output: type: file description: Contains variants in repeat regions pattern: "*.repeats.vcf" + ontologies: [] repeats_vcf_gz: - - meta: type: map @@ -941,6 +1050,8 @@ output: type: file description: Gzipped VCF file with variants in repeat regions pattern: "*.repeats.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 repeats_vcf_gz_tbi: - - meta: type: map @@ -951,6 +1062,7 @@ output: type: file description: Index file for the gzipped repeats VCF pattern: "*.repeats.vcf.gz.tbi" + ontologies: [] roh_bed: - - meta: type: map @@ -961,6 +1073,7 @@ output: type: file description: Contains regions of homozygosity pattern: "*.roh.bed" + ontologies: [] roh_metrics_csv: - - meta: type: map @@ -971,6 +1084,8 @@ output: type: file description: Contains metrics related to regions of homozygosity pattern: "*.roh_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 sam: - - meta: type: map @@ -981,6 +1096,7 @@ output: type: file description: Contains aligned read data in SAM format pattern: "*.sam" + ontologies: [] seg: - - meta: type: map @@ -991,6 +1107,7 @@ output: type: file description: Contains segmentation of genomic regions pattern: "*.seg" + ontologies: [] seg_bw: - - meta: type: map @@ -1001,6 +1118,7 @@ output: type: file description: BigWig file containing segmentation data pattern: "*.seg.bw" + ontologies: [] seg_c_partial_y: - - meta: type: map @@ -1011,6 +1129,7 @@ output: type: file description: Contains partial Y chromosome segmentation data pattern: "*.seg.c.partial.Y" + ontologies: [] seg_called: - - meta: type: map @@ -1021,6 +1140,7 @@ output: type: file description: Contains called segmentation data pattern: "*.seg.called" + ontologies: [] seg_called_merged: - - meta: type: map @@ -1031,6 +1151,7 @@ output: type: file description: Contains merged segmentation data pattern: "*.seg.called.merged" + ontologies: [] select_gvcf: - - meta: type: map @@ -1041,6 +1162,7 @@ output: type: file description: Contains selected genomic variants in GVCF format pattern: "*.select.gvcf" + ontologies: [] small_indel_dedup: - - meta: type: map @@ -1051,6 +1173,7 @@ output: type: file description: Contains deduplicated small indel variants pattern: "*.small_indel_dedup" + ontologies: [] smn_dedup: - - meta: type: map @@ -1061,6 +1184,7 @@ output: type: file description: Contains deduplicated SMN variants pattern: "*.smn_dedup" + ontologies: [] snperror_samples_log: - - meta: type: map @@ -1071,6 +1195,7 @@ output: type: file description: Log file containing information about SNP error sampling pattern: "*.snperror-sampler.log" + ontologies: [] sv_vcf: - - meta: type: map @@ -1081,6 +1206,7 @@ output: type: file description: VCF file containing structural variants pattern: "*.sv.vcf" + ontologies: [] sv_vcf_gz_tbi: - - meta: type: map @@ -1091,6 +1217,7 @@ output: type: file description: Index file for the gzipped SV VCF pattern: "*.sv.vcf.gz.tbi" + ontologies: [] sv_metrics_csv: - - meta: type: map @@ -1101,6 +1228,8 @@ output: type: file description: Contains metrics related to structural variants pattern: "*.sv_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 target_counts_bw: - - meta: type: map @@ -1111,6 +1240,7 @@ output: type: file description: BigWig file containing target counts pattern: "*.target.counts.bw" + ontologies: [] target_counts_diploid_bw: - - meta: type: map @@ -1121,6 +1251,7 @@ output: type: file description: BigWig file containing diploid target counts pattern: "*.target.counts.diploid.bw" + ontologies: [] target_counts_gc_corrected_gz: - - meta: type: map @@ -1131,6 +1262,8 @@ output: type: file description: Gzipped file containing GC-corrected target counts pattern: "*.target.counts.gc-corrected.gz" + ontologies: + - edam: http://edamontology.org/format_3989 target_counts_gz: - - meta: type: map @@ -1141,6 +1274,8 @@ output: type: file description: Gzipped file containing target counts pattern: "*.target.counts.gz" + ontologies: + - edam: http://edamontology.org/format_3989 targeted_json: - - meta: type: map @@ -1151,6 +1286,8 @@ output: type: file description: JSON file containing targeted sequencing information pattern: "*.targeted.json" + ontologies: + - edam: http://edamontology.org/format_3464 targeted_vcf_gz: - - meta: type: map @@ -1161,6 +1298,8 @@ output: type: file description: Gzipped VCF file containing targeted variants pattern: "*.targeted.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 time_metrics_csv: - - meta: type: map @@ -1171,6 +1310,8 @@ output: type: file description: Contains time metrics for the workflow pattern: "*.time_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 tn_bw: - - meta: type: map @@ -1181,6 +1322,7 @@ output: type: file description: BigWig file containing TN (Tumor Normal) data pattern: "*.tn.bw" + ontologies: [] tn_tsv_gz: - - meta: type: map @@ -1191,6 +1333,8 @@ output: type: file description: Contains TN data in gzipped TSV format pattern: "*.tn.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 trimmer_metrics_csv: - - meta: type: map @@ -1201,6 +1345,8 @@ output: type: file description: Contains metrics from the trimmer pattern: "*.trimmer_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 vc_hethom_ratio_metrics_csv: - - meta: type: map @@ -1211,6 +1357,8 @@ output: type: file description: Contains heterozygous to homozygous ratio metrics pattern: "*.vc_hethom_ratio_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 vc_metrics_csv: - - meta: type: map @@ -1221,6 +1369,8 @@ output: type: file description: Contains variant calling metrics pattern: "*.vc_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 vcf_gz: - - meta: type: map @@ -1231,6 +1381,8 @@ output: type: file description: Gzipped VCF file containing genomic variants pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 vcf_gz_md5sum: - - meta: type: map @@ -1241,6 +1393,7 @@ output: type: file description: MD5 checksum file for the gzipped VCF pattern: "*.vcf.gz.md5sum" + ontologies: [] vcf_gz_tbi: - - meta: type: map @@ -1251,6 +1404,7 @@ output: type: file description: Index file for the gzipped VCF pattern: "*.vcf.gz.tbi" + ontologies: [] wgs_contig_mean_cov_csv: - - meta: type: map @@ -1261,6 +1415,8 @@ output: type: file description: Contains WGS contig mean coverage metrics pattern: "*.wgs_contig_mean_cov.csv" + ontologies: + - edam: http://edamontology.org/format_3752 wgs_coverage_metrics_csv: - - meta: type: map @@ -1271,6 +1427,8 @@ output: type: file description: Contains WGS coverage metrics pattern: "*.wgs_coverage_metrics.csv" + ontologies: + - edam: http://edamontology.org/format_3752 wgs_fine_hist_csv: - - meta: type: map @@ -1281,6 +1439,8 @@ output: type: file description: Contains WGS fine histogram data pattern: "*.wgs_fine_hist.csv" + ontologies: + - edam: http://edamontology.org/format_3752 wgs_hist_csv: - - meta: type: map @@ -1291,6 +1451,8 @@ output: type: file description: Contains WGS histogram data pattern: "*.wgs_hist.csv" + ontologies: + - edam: http://edamontology.org/format_3752 wgs_overall_mean_cov_csv: - - meta: type: map @@ -1301,6 +1463,8 @@ output: type: file description: Contains WGS overall mean coverage metrics pattern: "*.wgs_overall_mean_cov.csv" + ontologies: + - edam: http://edamontology.org/format_3752 callability_bed: - - meta: type: map @@ -1311,6 +1475,7 @@ output: type: file description: BED file containing callability regions pattern: "*_callability.bed" + ontologies: [] chr_start_end_impute_phase_vcf_gz: - - meta: type: map @@ -1321,6 +1486,8 @@ output: type: file description: Gzipped VCF file containing phased imputed variants pattern: "*_chr_start-end.impute.phase.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 contig_mean_cov_csv: - - meta: type: map @@ -1331,6 +1498,8 @@ output: type: file description: Contains WGS contig mean coverage metrics pattern: "*_contig_mean_cov.csv" + ontologies: + - edam: http://edamontology.org/format_3752 cov_report_bed: - - meta: type: map @@ -1341,6 +1510,7 @@ output: type: file description: BED file containing coverage report pattern: "*_cov_report.bed" + ontologies: [] evidence: - - meta: type: map @@ -1351,6 +1521,7 @@ output: type: file description: Sorted BAM, CRAM or SAM file containing evidence reads pattern: "*_evidence.{b,cr,s}am" + ontologies: [] fine_hist_csv: - - meta: type: map @@ -1361,6 +1532,8 @@ output: type: file description: Contains fine histogram data pattern: "*_fine_hist.csv" + ontologies: + - edam: http://edamontology.org/format_3752 full_res_bed: - - meta: type: map @@ -1371,6 +1544,7 @@ output: type: file description: BED file containing full resolution data pattern: "*_full_res.bed" + ontologies: [] hist_csv: - - meta: type: map @@ -1381,6 +1555,8 @@ output: type: file description: Contains histogram data pattern: "*_hist.csv" + ontologies: + - edam: http://edamontology.org/format_3752 overall_mean_cov_csv: - - meta: type: map @@ -1391,6 +1567,8 @@ output: type: file description: Contains overall mean coverage metrics pattern: "*_overall_mean_cov.csv" + ontologies: + - edam: http://edamontology.org/format_3752 read_cov_report_bed: - - meta: type: map @@ -1401,6 +1579,7 @@ output: type: file description: BED file containing read coverage report pattern: "*_read_cov_report.bed" + ontologies: [] partitions_txt: - ./sort_spill/partitions.txt: type: file @@ -1419,28 +1598,28 @@ output: description: Candidate metrics pattern: "./sv/results/stats/candidate_metrics.csv" ontologies: - - edam: http://edamontology.org/format_3752 # CSV + - edam: http://edamontology.org/format_3752 diploidSV_sv_metrics_csv: - ./sv/results/stats/diploidSV.sv_metrics.csv: type: file description: Diploid SV metrics pattern: "./sv/results/stats/diploidSV.sv_metrics.csv" ontologies: - - edam: http://edamontology.org/format_3752 # CSV + - edam: http://edamontology.org/format_3752 graph_metrics_csv: - ./sv/results/stats/graph_metrics.csv: type: file description: Graph metrics pattern: "./sv/results/stats/graph_metrics.csv" ontologies: - - edam: http://edamontology.org/format_3752 # CSV + - edam: http://edamontology.org/format_3752 svCandidateGenerationStats_tsv: - ./sv/results/stats/svCandidateGenerationStats.tsv: type: file description: Structural variant candidate generation statistics pattern: "./sv/results/stats/svCandidateGenerationStats.tsv" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 svCandidateGenerationStats_xml: - ./sv/results/stats/svCandidateGenerationStats.xml: type: file @@ -1448,21 +1627,21 @@ output: format) pattern: "./sv/results/stats/svCandidateGenerationStats.xml" ontologies: - - edam: http://edamontology.org/format_2332 # XML + - edam: http://edamontology.org/format_2332 svLocusGraphStats_tsv: - ./sv/results/stats/svLocusGraphStats.tsv: type: file description: Structural variant locus graph statistics pattern: "./sv/results/stats/svLocusGraphStats.tsv" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 candidateSV_vcf_gz: - ./sv/results/variants/candidateSV.vcf.gz: type: file description: Candidate structural variants (VCF format) pattern: "./sv/results/variants/candidateSV.vcf.gz" ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 candidateSV_vcf_gz_tbi: - ./sv/results/variants/candidateSV.vcf.gz.tbi: type: file @@ -1475,7 +1654,7 @@ output: description: Gzipped VCF file containing diploid structural variants pattern: "./sv/results/variants/diploidSV.vcf.gz" ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 diploidSV_vcf_gz_tbi: - ./sv/results/variants/diploidSV.vcf.gz.tbi: type: file @@ -1488,7 +1667,7 @@ output: description: Alignment statistics in XML format pattern: "./sv/workspace/alignmentStats.xml" ontologies: - - edam: http://edamontology.org/format_2332 # XML + - edam: http://edamontology.org/format_2332 chromDepth_txt: - ./sv/workspace/chromDepth.txt: type: file @@ -1531,7 +1710,7 @@ output: description: Dragen time metrics pattern: "dragen.time_metrics.csv" ontologies: - - edam: http://edamontology.org/format_3752 # CSV + - edam: http://edamontology.org/format_3752 header_txt: - header.txt: type: file @@ -1556,7 +1735,7 @@ output: description: Streaming log files pattern: "streaming_log_*.csv" ontologies: - - edam: http://edamontology.org/format_3752 # CSV + - edam: http://edamontology.org/format_3752 usage_txt: - "*_usage.txt": type: file @@ -1569,13 +1748,27 @@ output: description: all output files pattern: "**" ontologies: [] + versions_dragen: + - - ${task.process}: + type: string + description: The name of the process + - dragen: + type: string + description: The name of the tool + - dragen --version 2>&1 | sed 's/^dragen Version //;s/ Hash.*//': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - dragen: + type: string + description: The name of the tool + - dragen --version 2>&1 | sed 's/^dragen Version //;s/ Hash.*//': + type: eval + description: The expression to obtain the version of the tool authors: - "@asr081" - "@marrip" diff --git a/modules/nf-core/dragen/germline/tests/main.nf.test b/modules/nf-core/dragen/germline/tests/main.nf.test index c4020c2b4ce6..68c7d9812d0a 100644 --- a/modules/nf-core/dragen/germline/tests/main.nf.test +++ b/modules/nf-core/dragen/germline/tests/main.nf.test @@ -65,7 +65,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out, - process.out.versions.collect{ path(it).yaml } + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) } diff --git a/modules/nf-core/dragen/germline/tests/main.nf.test.snap b/modules/nf-core/dragen/germline/tests/main.nf.test.snap index 366a5b45dd3c..27fda0409c13 100644 --- a/modules/nf-core/dragen/germline/tests/main.nf.test.snap +++ b/modules/nf-core/dragen/germline/tests/main.nf.test.snap @@ -147,13 +147,14 @@ "20251120_usage.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "141": [ - [ - "20251120_usage.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "versions.yml:md5,0800f35b86c052ff03f30ce186300e7e" - ] + "20251120_usage.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "142": [ - "versions.yml:md5,0800f35b86c052ff03f30ce186300e7e" + [ + "DRAGEN", + "dragen", + "bash: line 1: dragen: command not found" + ] ], "15": [ @@ -444,10 +445,7 @@ ], "all": [ - [ - "20251120_usage.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "versions.yml:md5,0800f35b86c052ff03f30ce186300e7e" - ] + "20251120_usage.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ], "baf_bedgraph_gz": [ @@ -848,8 +846,12 @@ "vcf_gz_tbi": [ ], - "versions": [ - "versions.yml:md5,0800f35b86c052ff03f30ce186300e7e" + "versions_dragen": [ + [ + "DRAGEN", + "dragen", + "bash: line 1: dragen: command not found" + ] ], "wgs_contig_mean_cov_csv": [ @@ -867,18 +869,20 @@ ] }, - [ - { - "DRAGEN": { - "dragen": "stub" - } - } - ] + { + "versions_dragen": [ + [ + "DRAGEN", + "dragen", + "bash: line 1: dragen: command not found" + ] + ] + } ], + "timestamp": "2026-03-13T16:29:08.483198173", "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-10-23T13:05:07.784959115" + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } } } \ No newline at end of file