diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d5eec807e..9f996af5dd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet - [1743](https://github.com/nf-core/sarek/pull/1743) - Add setup java 17 in GHA for latest Nextflow version - [1745](https://github.com/nf-core/sarek/pull/1745) - Fix bug where workflow can hang if the email parameter is set +- [1746](https://github.com/nf-core/sarek/pull/1746) - Fix Sentieon module inputs ### Removed diff --git a/conf/modules/aligner.config b/conf/modules/aligner.config index 5f44e199b0..70926d573a 100644 --- a/conf/modules/aligner.config +++ b/conf/modules/aligner.config @@ -30,11 +30,11 @@ process { } withName: 'SENTIEON_BWAMEM' { + ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]).concat('.bam') : "${meta.id}.sorted.bam" } ext.when = { params.aligner == 'sentieon-bwamem' } } withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM' { - ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" } publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/preprocessing/" }, @@ -56,6 +56,7 @@ process { } withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN' { + ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" } // Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof // However if it's skipped, reads need to be coordinate-sorted // Only name sort if Spark for Markduplicates + duplicate marking is not skipped diff --git a/conf/modules/sentieon_dedup.config b/conf/modules/sentieon_dedup.config index df52c3bb95..35f89720f7 100644 --- a/conf/modules/sentieon_dedup.config +++ b/conf/modules/sentieon_dedup.config @@ -16,7 +16,7 @@ process { withName: 'SENTIEON_DEDUP' { - ext.prefix = { "${meta.id}.dedup" } + ext.prefix = { "${meta.id}.dedup.cram" } ext.when = { params.tools && params.tools.split(',').contains('sentieon_dedup') } publishDir = [ [ diff --git a/modules.json b/modules.json index 75fec0dbc7..c2e28076ab 100644 --- a/modules.json +++ b/modules.json @@ -257,7 +257,8 @@ "gatk4/intervallisttobed": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff" }, "gatk4/learnreadorientationmodel": { "branch": "master", diff --git a/modules/local/create_intervals_bed/main.nf b/modules/local/create_intervals_bed/main.nf index 6a3c9c5a47..2bf36190e4 100644 --- a/modules/local/create_intervals_bed/main.nf +++ b/modules/local/create_intervals_bed/main.nf @@ -72,4 +72,18 @@ process CREATE_INTERVALS_BED { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${intervals.baseName}" + def metrics = task.ext.metrics ?: "${prefix}.metrics" + // def prefix_basename = prefix.substring(0, prefix.lastIndexOf(".")) + + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff b/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff new file mode 100644 index 0000000000..03086949c6 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff @@ -0,0 +1,27 @@ +Changes in module 'nf-core/gatk4/intervallisttobed' +'modules/nf-core/gatk4/intervallisttobed/environment.yml' is unchanged +'modules/nf-core/gatk4/intervallisttobed/meta.yml' is unchanged +Changes in 'gatk4/intervallisttobed/main.nf': +--- modules/nf-core/gatk4/intervallisttobed/main.nf ++++ modules/nf-core/gatk4/intervallisttobed/main.nf +@@ -40,4 +40,18 @@ + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ ++ ++ stub: ++ def prefix = task.ext.prefix ?: "${meta.id}.cram" ++ def metrics = task.ext.metrics ?: "${prefix}.metrics" ++ def prefix_basename = prefix.substring(0, prefix.lastIndexOf(".")) ++ ++ """ ++ touch ${prefix}.bed ++ ++ cat <<-END_VERSIONS > versions.yml ++ "${task.process}": ++ gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') ++ END_VERSIONS ++ """ + } + +************************************************************ diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf index 2f6893c0ca..743bb3413a 100644 --- a/modules/nf-core/gatk4/intervallisttobed/main.nf +++ b/modules/nf-core/gatk4/intervallisttobed/main.nf @@ -40,4 +40,18 @@ process GATK4_INTERVALLISTTOBED { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}.cram" + def metrics = task.ext.metrics ?: "${prefix}.metrics" + def prefix_basename = prefix.substring(0, prefix.lastIndexOf(".")) + + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ } diff --git a/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf b/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf index 23d0d8675a..0ac47a1e1e 100644 --- a/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf +++ b/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf @@ -36,7 +36,7 @@ workflow BAM_JOINT_CALLING_GERMLINE_SENTIEON { .map{ meta, gvcf, tbi, intervals -> [ [ id:'joint_variant_calling', intervals_name:intervals.baseName, num_intervals:meta.num_intervals ], gvcf, tbi, intervals ] } .groupTuple(by:[0, 3]) - SENTIEON_GVCFTYPER(sentieon_input, fasta.map{meta, it -> [ it ]}, fai.map{meta, it -> [ it ]}, dbsnp, dbsnp_tbi) + SENTIEON_GVCFTYPER(sentieon_input, fasta, fai, dbsnp, dbsnp_tbi) BCFTOOLS_SORT(SENTIEON_GVCFTYPER.out.vcf_gz) diff --git a/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf b/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf index 1f0d59e522..5c1f1338d2 100644 --- a/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf +++ b/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf @@ -48,9 +48,9 @@ workflow BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER { emit_vcf = lst.size() > 0 ? lst[0] : '' SENTIEON_HAPLOTYPER( - cram_intervals_for_sentieon, - fasta.map{ meta, it -> it }, - fasta_fai.map{ meta, it -> it }, + cram_intervals_for_sentieon.map{ meta, cram, crai, intervals, num_intervals -> [ meta, cram, crai, intervals, [] ]}, + fasta, + fasta_fai, dbsnp, dbsnp_tbi, emit_vcf, diff --git a/tests/sentieon.nf.test b/tests/sentieon.nf.test new file mode 100644 index 0000000000..2a774e0803 --- /dev/null +++ b/tests/sentieon.nf.test @@ -0,0 +1,48 @@ +nextflow_pipeline { + + name "Test sentieon" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + tag "sentieon" + + test("stub") { + + tag "stub" + + options "-stub" + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + aligner = "sentieon-bwamem" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path, + // All cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap new file mode 100644 index 0000000000..26bd91e7ff --- /dev/null +++ b/tests/sentieon.nf.test.snap @@ -0,0 +1,301 @@ +{ + "stub": { + "content": [ + 23, + { + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_MARKDUPLICATES": { + "gatk4": "4.5.0.0", + "samtools": "1.19.2" + }, + "INDEX_CRAM": { + "samtools": 1.21 + }, + "MOSDEPTH": { + "mosdepth": "0.3.8" + }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, + "SENTIEON_BWAMEM": { + "sentieon": 202308.03, + "bwa": "0.7.17-r1188" + }, + "STRELKA_SINGLE": { + "strelka": "2.9.10" + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "csv/markduplicates.csv", + "csv/markduplicates_no_table.csv", + "csv/recalibrated.csv", + "csv/variantcalled.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "preprocessing", + "preprocessing/markduplicates", + "preprocessing/markduplicates/test", + "preprocessing/markduplicates/test/test.cram", + "preprocessing/markduplicates/test/test.cram.crai", + "preprocessing/recal_table", + "preprocessing/recal_table/test", + "preprocessing/recal_table/test/test.recal.table", + "preprocessing/recalibrated", + "preprocessing/recalibrated/test", + "preprocessing/recalibrated/test/test.recal.cram", + "preprocessing/recalibrated/test/test.recal.cram.crai", + "reference", + "reports", + "reports/bcftools", + "reports/bcftools/strelka", + "reports/bcftools/strelka/test", + 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