diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bb09e1f2..cdc6de93 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -25,7 +25,7 @@ jobs: matrix: NXF_VER: - "24.10.0" - - "latest-everything" + - "latest-stable" filter: - "process" - "workflow" diff --git a/.nf-core.yml b/.nf-core.yml index 2b9576c9..42ea59f0 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,32 +2,32 @@ bump_version: lint: actions_ci: false files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - .github/workflows/template_version_comment.yml - - docs/README.md + - CODE_OF_CONDUCT.md + - assets/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - .github/workflows/template_version_comment.yml + - docs/README.md files_unchanged: - - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - CODE_OF_CONDUCT.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - .prettierignore + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - CODE_OF_CONDUCT.md + - .github/ISSUE_TEMPLATE/bug_report.yml + - .prettierignore multiqc_config: - - report_comment + - report_comment nextflow_config: - - custom_config - - manifest.name - - manifest.homePage - - validation.help.afterText - - validation.summary.afterText + - custom_config + - manifest.name + - manifest.homePage + - validation.help.afterText + - validation.summary.afterText subworkflow_changes: false nf_core_version: 3.0.2 repository_type: pipeline @@ -41,6 +41,6 @@ template: org: nf-cmgg outdir: . skip_features: - - fastqc - - is_nfcore - version: 1.9.1 + - fastqc + - is_nfcore + version: 1.9.2 diff --git a/CHANGELOG.md b/CHANGELOG.md index 90acd586..598faa39 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.9.2 - New Nieuwkerke - [January 22 2025] + +## Changes + +1. The pipeline now also outputs the per-base coverage BED file generated by mosdepth per sample +2. Add the `--disable_hc_dict_validation` parameter that disables sequence dictionary validation in HaplotypeCaller + ## v1.9.1 - Nice Nieuwkerke - [January 16 2025] ### Changes diff --git a/conf/modules.config b/conf/modules.config index 138ba4f1..3460d37f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -44,7 +44,7 @@ process { withName: "^.*CRAM_PREPARE_SAMTOOLS_BEDTOOLS:MOSDEPTH\$" { ext.args = [ - "--quantize 0:1:${params.min_callable_coverage - 1}: --mapq 1 --flag 1804 --no-per-base", + "--quantize 0:1:${params.min_callable_coverage - 1}: --mapq 1 --flag 1804", params.mosdepth_slow ? "" : "--fast-mode" ].join(" ") } @@ -79,7 +79,8 @@ process { '-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90', '-G StandardAnnotation -G StandardHCAnnotation -G AS_StandardAnnotation', params.dragstr ? '--dragen-mode' : '', - params.hc_phasing ? '' : '--do-not-run-physical-phasing' + params.hc_phasing ? '' : '--do-not-run-physical-phasing', + params.disable_hc_dict_validation ? '--disable-sequence-dictionary-validation' : '' ].join(" ") } } diff --git a/conf/seqplorer.config b/conf/seqplorer.config index ccac085a..b0e39b81 100644 --- a/conf/seqplorer.config +++ b/conf/seqplorer.config @@ -5,18 +5,19 @@ */ params { - filter = true - normalize = true - gemini = true + filter = true + normalize = true + gemini = true + disable_hc_dict_validation = true - vcfanno = true - annotate = true - vep_merged = true - vep_spliceai = true - vep_mastermind = true - vep_eog = true - vep_spliceregion = true + vcfanno = true + annotate = true + vep_merged = true + vep_spliceai = true + vep_mastermind = true + vep_eog = true + vep_spliceregion = true - vcfanno_config = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/main/conf/Hsapiens/vcfanno/cmgg_vcfanno.toml" - vcfanno_resources = "${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz.tbi" + vcfanno_config = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/main/conf/Hsapiens/vcfanno/cmgg_vcfanno.toml" + vcfanno_resources = "${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz.tbi" } diff --git a/docs/output.md b/docs/output.md index facf11d9..eb836d60 100644 --- a/docs/output.md +++ b/docs/output.md @@ -34,6 +34,8 @@ To explain the structure of the output directory, a simple example run consistin │ │ ├── sample1..bcftools_stats.txt #(17)! │ │ ├── sample1..g.vcf.gz #(18)! │ │ ├── sample1..g.vcf.gz.tbi #(19)! +│ │ ├── sample1.per-base.bed.gz #(33)! +│ │ ├── sample1.per-base.bed.gz.csi #(34)! │ │ └── validation #(20)! │ │ └── #(21)! │ │ ├── ... #(22)! @@ -118,3 +120,7 @@ To explain the structure of the output directory, a simple example run consistin 31. This file contains a list of all tools used in the pipeline and their versions 32. The samplesheet used to run this pipeline run + +33. The per-base coverage BED file generated by Mosdepth + +34. The index of the per-base coverage BED file generated by Mosdepth diff --git a/main.nf b/main.nf index 7869d843..8f3523cf 100644 --- a/main.nf +++ b/main.nf @@ -99,10 +99,6 @@ workflow { if(!(caller in GlobalVariables.availableCallers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${GlobalVariables.availableCallers}")} } - if (params.output_suffix && callers.size() > 1) { - error("Cannot use --output_suffix with more than one caller") - } - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CONFIG FILES @@ -219,6 +215,7 @@ workflow { publish: ch_gvcfs_out >> 'gvcfs' GERMLINE.out.single_beds >> 'single_beds' + GERMLINE.out.perbase_beds >> 'perbase_beds' GERMLINE.out.validation >> 'validation' GERMLINE.out.gvcf_reports >> 'gvcf_reports' GERMLINE.out.genomicsdb >> 'genomicsdb' @@ -245,6 +242,14 @@ output { 'single_beds' { path { meta, _bed -> { _file -> "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.bed" } } } + 'perbase_beds' { + path { meta, bed, _csi -> { file -> + if(file == bed.name) { + return "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.per-base.bed.gz" + } + return "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.per-base.bed.gz.csi" + } } + } 'validation' { path { meta, _report -> { file -> "${meta.family}/${meta.id}_${params.unique_out}/validation/${meta.caller}/${file}" } } } diff --git a/nextflow.config b/nextflow.config index 346e95d2..36bd916e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -41,6 +41,7 @@ params { mosdepth_slow = false merge_distance = 100000 updio_common_cnvs = null + disable_hc_dict_validation = false // VEP plugins to use vep_dbnsfp = false @@ -276,7 +277,7 @@ manifest { description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data""" mainScript = 'main.nf' nextflowVersion = '!>=24.10.0' - version = '1.9.1' + version = '1.9.2' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 4e061f2a..6861302d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -331,6 +331,10 @@ "type": "string", "description": "Don't change this value", "hidden": true + }, + "disable_hc_dict_validation": { + "type": "boolean", + "description": "Disable the sequence dictionary validation in HaplotypeCaller" } } }, diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf index 62b241ee..5379141d 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf +++ b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf @@ -151,6 +151,8 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { ch_fasta ) ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first()) + def ch_perbase_beds = MOSDEPTH.out.per_base_bed + .join(MOSDEPTH.out.per_base_csi, failOnMismatch: true, failOnDuplicate:true) def ch_beds_to_filter = ch_ready_rois .join(MOSDEPTH.out.quantized_bed, failOnDuplicate:true, failOnMismatch:true) @@ -181,9 +183,10 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { .mix(BEDTOOLS_INTERSECT.out.intersect) emit: - ready_crams = ch_ready_crams // [ val(meta), path(cram), path(crai) ] - ready_bams = ch_ready_bams // [ val(meta), path(bam), path(bai) ] - ready_beds = ch_ready_beds // [ val(meta), path(bed) ] - versions = ch_versions // [ path(versions) ] - reports = ch_reports // [ path(reports) ] + ready_crams = ch_ready_crams // [ val(meta), path(cram), path(crai) ] + ready_bams = ch_ready_bams // [ val(meta), path(bam), path(bai) ] + ready_beds = ch_ready_beds // [ val(meta), path(bed) ] + perbase_beds = ch_perbase_beds // [ val(meta), path(bed), path(csi) ] + versions = ch_versions // [ path(versions) ] + reports = ch_reports // [ path(reports) ] } diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test b/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test index cdb50e44..81785a4d 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test +++ b/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test @@ -48,6 +48,7 @@ nextflow_workflow { [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ] }, workflow.out.ready_beds, + workflow.out.perbase_beds, workflow.out.reports ).match() } ) @@ -95,6 +96,7 @@ nextflow_workflow { [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ] }, workflow.out.ready_beds, + workflow.out.perbase_beds, workflow.out.reports ).match() } ) @@ -142,6 +144,7 @@ nextflow_workflow { [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ] }, workflow.out.ready_beds, + workflow.out.perbase_beds, workflow.out.reports ).match() } ) @@ -196,6 +199,7 @@ nextflow_workflow { [ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ] }, workflow.out.ready_beds, + workflow.out.perbase_beds, workflow.out.reports ).match() } ) diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test.snap b/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test.snap index 64b29194..5849a29e 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test.snap +++ b/subworkflows/local/cram_prepare_samtools_bedtools/tests/main.nf.test.snap @@ -39,15 +39,28 @@ "NA24143.intersect.bed:md5,b87069698afefb15282d069e56110046" ] ], + [ + [ + { + "id": "NA24143", + "sample": "NA24143", + "family": "Ashkenazim", + "family_samples": "NA24143", + "duplicate_count": 1 + }, + "NA24143.per-base.bed.gz:md5,2f773324021d6d1b18c87af240d1a18f", + "NA24143.per-base.bed.gz.csi:md5,fe996e285822f6126adcdca8b7517058" + ] + ], [ ] ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-14T16:07:03.620603158" + "timestamp": "2025-01-22T13:39:12.575142149" }, "cram_prepare_samtools_bedtools - default - WES": { "content": [ @@ -79,15 +92,28 @@ "NA24143.intersect.bed:md5,b87069698afefb15282d069e56110046" ] ], + [ + [ + { + "id": "NA24143", + "sample": "NA24143", + "family": "Ashkenazim", + "family_samples": "NA24143", + "duplicate_count": 1 + }, + "NA24143.per-base.bed.gz:md5,2f773324021d6d1b18c87af240d1a18f", + "NA24143.per-base.bed.gz.csi:md5,fe996e285822f6126adcdca8b7517058" + ] + ], [ ] ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-14T16:07:24.688580575" + "timestamp": "2025-01-22T13:39:30.958080052" }, "cram_prepare_samtools_bedtools - default - WGS": { "content": [ @@ -119,15 +145,28 @@ "NA24143.filter.bed:md5,85a5568a6976ed455caa712991b30ac2" ] ], + [ + [ + { + "id": "NA24143", + "sample": "NA24143", + "family": "Ashkenazim", + "family_samples": "NA24143", + "duplicate_count": 1 + }, + "NA24143.per-base.bed.gz:md5,2f773324021d6d1b18c87af240d1a18f", + "NA24143.per-base.bed.gz.csi:md5,fe996e285822f6126adcdca8b7517058" + ] + ], [ ] ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-14T16:06:42.311563291" + "timestamp": "2025-01-22T13:38:51.625657423" }, "cram_prepare_samtools_bedtools - default - merge": { "content": [ @@ -169,14 +208,27 @@ "NA24143.intersect.bed:md5,b87069698afefb15282d069e56110046" ] ], + [ + [ + { + "id": "NA24143", + "sample": "NA24143", + "family": "Ashkenazim", + "family_samples": "NA24143", + "duplicate_count": 2 + }, + "NA24143.per-base.bed.gz:md5,85e799ea056ba8d127115e012adcbe7a", + "NA24143.per-base.bed.gz.csi:md5,3f40731dbdbef353385d04f51feb43b3" + ] + ], [ ] ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-14T16:08:20.712943795" + "timestamp": "2025-01-22T13:40:12.40700375" } } \ No newline at end of file diff --git a/tests/pipeline/callers/main.nf.test.snap b/tests/pipeline/callers/main.nf.test.snap index dcd0e17c..bc07f896 100644 --- a/tests/pipeline/callers/main.nf.test.snap +++ b/tests/pipeline/callers/main.nf.test.snap @@ -6,14 +6,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -26,9 +32,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:05:33.245638727" + "timestamp": "2025-01-22T13:43:40.835272376" }, "pipeline_callers - vardict + haplotypecaller": { "content": [ @@ -37,14 +43,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -72,16 +84,22 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:09:45.604865258" + "timestamp": "2025-01-22T13:44:52.575355189" }, "pipeline_callers - vardict": { "content": [ [ "Ashkenazim/NA24143__/NA24143.bed", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/NA24143.vardict.ped", "Ashkenazim/output__/NA24143.vardict.vcf.gz", "Ashkenazim/output__/NA24143.vardict.vcf.gz.tbi", @@ -103,8 +121,8 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:02:38.547566464" + "timestamp": "2025-01-22T13:42:31.160189572" } } \ No newline at end of file diff --git a/tests/pipeline/default/main.nf.test.snap b/tests/pipeline/default/main.nf.test.snap index 3bf2a32c..8ffcae00 100644 --- a/tests/pipeline/default/main.nf.test.snap +++ b/tests/pipeline/default/main.nf.test.snap @@ -6,14 +6,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -26,8 +32,8 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T13:55:37.532795185" + "timestamp": "2025-01-22T13:45:59.679120723" } } \ No newline at end of file diff --git a/tests/pipeline/variations/main.nf.test.snap b/tests/pipeline/variations/main.nf.test.snap index 95999b13..3c6f7feb 100644 --- a/tests/pipeline/variations/main.nf.test.snap +++ b/tests/pipeline/variations/main.nf.test.snap @@ -6,14 +6,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim_haplotypecaller_genomicsdb", "_/multiqc_report.html", "_/samplesheet.csv" @@ -21,9 +27,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:28:35.043452694" + "timestamp": "2025-01-22T13:52:11.995335577" }, "pipeline_variations - filter": { "content": [ @@ -32,14 +38,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -52,9 +64,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:24:24.556080575" + "timestamp": "2025-01-22T13:50:35.751317235" }, "pipeline_variations - annotate + vcfanno": { "content": [ @@ -63,14 +75,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -83,9 +101,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:21:15.80188879" + "timestamp": "2025-01-22T13:49:26.904699766" }, "pipeline_variations - annotate": { "content": [ @@ -94,14 +112,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -114,9 +138,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:17:45.975261786" + "timestamp": "2025-01-22T13:48:06.520399436" }, "pipeline_variations - only_call": { "content": [ @@ -125,23 +149,29 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "_/multiqc_report.html", "_/samplesheet.csv" ] ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:26:32.219983438" + "timestamp": "2025-01-22T13:51:23.297404025" }, "pipeline_variations - automap": { "content": [ @@ -150,14 +180,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -182,8 +218,8 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:31:35.104677632" + "timestamp": "2025-01-22T13:53:25.411254268" } } \ No newline at end of file diff --git a/tests/pipeline/variations2/main.nf.test.snap b/tests/pipeline/variations2/main.nf.test.snap index e0053c6b..a127abcc 100644 --- a/tests/pipeline/variations2/main.nf.test.snap +++ b/tests/pipeline/variations2/main.nf.test.snap @@ -6,14 +6,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -26,9 +32,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:48:10.189725508" + "timestamp": "2025-01-22T13:58:59.743496229" }, "pipeline_variations - normalize": { "content": [ @@ -37,14 +43,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -57,9 +69,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:34:50.228561252" + "timestamp": "2025-01-22T13:54:32.376500134" }, "pipeline_variations - updio": { "content": [ @@ -68,14 +80,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", "Ashkenazim/output__/Ashkenazim.haplotypecaller.vcf.gz", @@ -88,9 +106,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:38:05.475938734" + "timestamp": "2025-01-22T13:55:38.269618437" }, "pipeline_variations - gemini": { "content": [ @@ -99,14 +117,20 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24149__/NA24149.bed", "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24385__/NA24385.bed", "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/output__/Ashkenazim.haplotypecaller.bed", "Ashkenazim/output__/Ashkenazim.haplotypecaller.db", "Ashkenazim/output__/Ashkenazim.haplotypecaller.ped", @@ -120,9 +144,9 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:41:11.213707091" + "timestamp": "2025-01-22T13:56:43.936046521" }, "pipeline_variations - validate": { "content": [ @@ -131,6 +155,8 @@ "Ashkenazim/NA24143__/NA24143.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24143__/NA24143.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz", + "Ashkenazim/NA24143__/NA24143.per-base.bed.gz.csi", "Ashkenazim/NA24143__/validation/haplotypecaller/NA24143.fn.vcf.gz", "Ashkenazim/NA24143__/validation/haplotypecaller/NA24143.fn.vcf.gz.tbi", "Ashkenazim/NA24143__/validation/haplotypecaller/NA24143.fp.vcf.gz", @@ -154,6 +180,8 @@ "Ashkenazim/NA24149__/NA24149.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24149__/NA24149.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz", + "Ashkenazim/NA24149__/NA24149.per-base.bed.gz.csi", "Ashkenazim/NA24149__/validation/haplotypecaller/NA24149.fn.vcf.gz", "Ashkenazim/NA24149__/validation/haplotypecaller/NA24149.fn.vcf.gz.tbi", "Ashkenazim/NA24149__/validation/haplotypecaller/NA24149.fp.vcf.gz", @@ -177,6 +205,8 @@ "Ashkenazim/NA24385__/NA24385.haplotypecaller.bcftools_stats.txt", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz", "Ashkenazim/NA24385__/NA24385.haplotypecaller.g.vcf.gz.tbi", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz", + "Ashkenazim/NA24385__/NA24385.per-base.bed.gz.csi", "Ashkenazim/NA24385__/validation/haplotypecaller/NA24385.fn.vcf.gz", "Ashkenazim/NA24385__/validation/haplotypecaller/NA24385.fn.vcf.gz.tbi", "Ashkenazim/NA24385__/validation/haplotypecaller/NA24385.fp.vcf.gz", @@ -208,8 +238,8 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nextflow": "24.10.3" }, - "timestamp": "2024-11-13T14:44:54.946386845" + "timestamp": "2025-01-22T13:57:55.547343728" } } \ No newline at end of file diff --git a/workflows/germline.nf b/workflows/germline.nf index 4eafdef3..5508df4f 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -417,6 +417,7 @@ workflow GERMLINE { ) ch_versions = ch_versions.mix(CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.versions) def ch_single_beds = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_beds + def ch_perbase_beds = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.perbase_beds // // Split the BED files @@ -895,6 +896,7 @@ workflow GERMLINE { gemini = ch_final_dbs // channel: [ val(meta), path(db) ] peds = ch_final_peds // channel: [ val(meta), path(ped) ] single_beds = ch_single_beds // channel: [ val(meta), path(bed) ] + perbase_beds = ch_perbase_beds // channel: [ val(meta), path(bed), path(csi) ] joint_beds = ch_joint_beds // channel: [ val(meta), path(bed) ] final_reports = ch_final_reports // channel: [ val(meta), path(report) ] gvcf_reports = ch_gvcf_reports // channel: [ val(meta), path(report) ]