From f549c759ff9ebd9e26ecb89b95c0cda72401a5ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20B=C3=A4uerle?= <45968370+famosab@users.noreply.github.com> Date: Thu, 16 Jan 2025 21:08:59 +0100 Subject: [PATCH] port parabricks/deepvariant to nf-test (#6995) * port to nf-test * remove * update test yaml * swap to nextflow config * finalize * revert changes to nf-test config * revert changes to nf-test config * add to conda_skip * add tag gpu * Update modules/nf-core/parabricks/deepvariant/tests/nextflow.config * Update modules/nf-core/parabricks/deepvariant/main.nf * fix tests and add myself as maintainer to other modules * fix meta * add isssue to comment * remove conda skip * update snap --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/parabricks/applybqsr/meta.yml | 1 + modules/nf-core/parabricks/dbsnp/meta.yml | 2 + .../nf-core/parabricks/deepvariant/main.nf | 22 +- .../nf-core/parabricks/deepvariant/meta.yml | 14 +- .../parabricks/deepvariant/tests/main.nf.test | 223 +++++++ .../deepvariant/tests/main.nf.test.snap | 566 ++++++++++++++++++ .../deepvariant/tests/nextflow.config | 7 + .../nf-core/parabricks/genotypegvcf/meta.yml | 2 + modules/nf-core/parabricks/indexgvcf/meta.yml | 2 + .../nf-core/parabricks/mutectcaller/meta.yml | 2 + tests/config/pytest_modules.yml | 3 - .../nf-core/parabricks/deepvariant/main.nf | 55 -- .../parabricks/deepvariant/nextflow.config | 8 - .../nf-core/parabricks/deepvariant/test.yml | 29 - .../deepvariant/test_GPU_config.txt | 14 - .../parabricks/deepvariant/test_GPU_yml.txt | 29 - 16 files changed, 829 insertions(+), 150 deletions(-) create mode 100644 modules/nf-core/parabricks/deepvariant/tests/main.nf.test create mode 100644 modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap create mode 100644 modules/nf-core/parabricks/deepvariant/tests/nextflow.config delete mode 100644 tests/modules/nf-core/parabricks/deepvariant/main.nf delete mode 100644 tests/modules/nf-core/parabricks/deepvariant/nextflow.config delete mode 100644 tests/modules/nf-core/parabricks/deepvariant/test.yml delete mode 100644 tests/modules/nf-core/parabricks/deepvariant/test_GPU_config.txt delete mode 100644 tests/modules/nf-core/parabricks/deepvariant/test_GPU_yml.txt diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml index 22f0c4c2067..3bf25c6832f 100644 --- a/modules/nf-core/parabricks/applybqsr/meta.yml +++ b/modules/nf-core/parabricks/applybqsr/meta.yml @@ -88,3 +88,4 @@ authors: - "@bsiranosian" maintainers: - "@bsiranosian" + - "@famosab" \ No newline at end of file diff --git a/modules/nf-core/parabricks/dbsnp/meta.yml b/modules/nf-core/parabricks/dbsnp/meta.yml index 095110cf45e..fe363cdecf8 100644 --- a/modules/nf-core/parabricks/dbsnp/meta.yml +++ b/modules/nf-core/parabricks/dbsnp/meta.yml @@ -50,3 +50,5 @@ output: pattern: "versions.yml" authors: - "@Furentsu" +maintainers: + - "@famosab" \ No newline at end of file diff --git a/modules/nf-core/parabricks/deepvariant/main.nf b/modules/nf-core/parabricks/deepvariant/main.nf index ac18b72f3ad..8c8c1d7dbca 100644 --- a/modules/nf-core/parabricks/deepvariant/main.nf +++ b/modules/nf-core/parabricks/deepvariant/main.nf @@ -1,40 +1,41 @@ process PARABRICKS_DEEPVARIANT { tag "$meta.id" label 'process_high' + label 'process_gpu' + stageInMode 'copy' // needed by the module to work properly can be removed when fixed upstream - Issue #7226 - container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1" + container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1" input: tuple val(meta), path(input), path(input_index), path(interval_file) tuple val(ref_meta), path(fasta) output: - tuple val(meta), path("*.vcf"), emit: vcf - path "versions.yml", emit: versions + tuple val(meta), path("*.vcf"), optional: true, emit: vcf + tuple val(meta), path("*.g.vcf.gz"), optional: true, emit: gvcf + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { exit 1, "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead." } - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def output_file = args =~ "gvcf" ? "${prefix}.g.vcf" : "${prefix}.vcf" + def output_file = ("--gvcf" =~ task.ext.args)? "${prefix}.g.vcf.gz" : "${prefix}.vcf" def interval_file_command = interval_file ? interval_file.collect{"--interval-file $it"}.join(' ') : "" + def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : '' """ - pbrun \\ deepvariant \\ --ref $fasta \\ --in-bam $input \\ --out-variants $output_file \\ $interval_file_command \\ - --num-gpus $task.accelerator.request \\ + $num_gpus \\ $args cat <<-END_VERSIONS > versions.yml @@ -44,11 +45,10 @@ process PARABRICKS_DEEPVARIANT { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def output_file = args =~ "gvcf" ? "${prefix}.g.vcf" : "${prefix}.vcf" + def output_cmd = ("--gvcf" =~ task.ext.args)? "echo '' | gzip > ${prefix}.g.vcf.gz" : "touch ${prefix}.vcf" """ - touch $output_file + $output_cmd cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/parabricks/deepvariant/meta.yml b/modules/nf-core/parabricks/deepvariant/meta.yml index 55998ea65e9..21a55a47ef0 100644 --- a/modules/nf-core/parabricks/deepvariant/meta.yml +++ b/modules/nf-core/parabricks/deepvariant/meta.yml @@ -53,8 +53,18 @@ output: e.g. [ id:'test' ] - "*.vcf": type: file - description: Variant file. + description: vcf file created with deepvariant (does not support .gz for normal vcf), optional pattern: "*.vcf" + - gvcf: + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.g.vcf.gz": + type: file + description: bgzipped gvcf created with deepvariant, optional + pattern: "*.g.vcf.gz" - versions: - versions.yml: type: file @@ -62,3 +72,5 @@ output: pattern: "versions.yml" authors: - "@bsiranosian" +maintainers: + - "@famosab" diff --git a/modules/nf-core/parabricks/deepvariant/tests/main.nf.test b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test new file mode 100644 index 00000000000..e2f448d3f78 --- /dev/null +++ b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test @@ -0,0 +1,223 @@ +nextflow_process { + + name "Test Process PARABRICKS_DEEPVARIANT" + script "../main.nf" + process "PARABRICKS_DEEPVARIANT" + + tag "modules" + tag "modules_nfcore" + tag "parabricks" + tag "parabricks/deepvariant" + tag "gpu" + + test("human - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + [], // bam.bai not needed unless using intervals + [] + ] + input[1] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.getVariantsAsStrings(100), + process.out.versions, + path(process.out.versions[0]).yaml + ).match() } + ) + } + + } + + test("human - bam - intervals") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) + ] + input[1] = [ + [ id:'ref'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.getVariantsAsStrings(100), + process.out.versions, + path(process.out.versions[0]).yaml + ).match() } + ) + } + + } + + test("human - bam - gvcf") { + + config './nextflow.config' + + when { + params { + module_args = '--gvcf' + } + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + [], // bam.bai not needed unless using intervals + [] + ] + input[1] = [ + [ id:'ref'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.gvcf[0][1]).vcf.getVariantsAsStrings(100), + process.out.versions, + path(process.out.versions[0]).yaml + ).match() + } + ) + } + + } + + test("human - bam - intervals - gvcf") { + + config './nextflow.config' + + when { + params { + module_args = '--gvcf' + } + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) + ] + input[1] = [ + [ id:'ref'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.gvcf[0][1]).vcf.getVariantsAsStrings(100), + process.out.versions, + path(process.out.versions[0]).yaml + ).match() + } + ) + } + + } + + test("human - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + [], // bam.bai not needed unless using intervals + [] + ] + input[1] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() } + ) + } + + } + + test("human - bam - intervals - gvcf - stub") { + + config './nextflow.config' + options "-stub" + + when { + params { + module_args = '--gvcf' + } + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) + ] + input[1] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap new file mode 100644 index 00000000000..3deda28f7c9 --- /dev/null +++ b/modules/nf-core/parabricks/deepvariant/tests/main.nf.test.snap @@ -0,0 +1,566 @@ +{ + "human - bam - intervals - gvcf": { + "content": [ + [ + 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"chr21\t5101001\t.\tG\t<*>\t0\t.\tEND=5102000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5102001\t.\tA\t<*>\t0\t.\tEND=5103000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5103001\t.\tG\t<*>\t0\t.\tEND=5104000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5104001\t.\tG\t<*>\t0\t.\tEND=5105000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5105001\t.\tC\t<*>\t0\t.\tEND=5106000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5106001\t.\tG\t<*>\t0\t.\tEND=5107000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5107001\t.\tC\t<*>\t0\t.\tEND=5108000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5108001\t.\tA\t<*>\t0\t.\tEND=5109000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0", + "chr21\t5109001\t.\tA\t<*>\t0\t.\tEND=5110000\tGT:GQ:MIN_DP:PL\t0/0:1:0:0,0,0" + ], + [ + "versions.yml:md5,c7bcf80d609e2951eb99f0b774cd2f6d" + ], + { + "PARABRICKS_DEEPVARIANT": { + "pbrun": "4.4.0-1" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2025-01-15T14:46:18.183309139" + } +} \ No newline at end of file diff --git a/modules/nf-core/parabricks/deepvariant/tests/nextflow.config b/modules/nf-core/parabricks/deepvariant/tests/nextflow.config new file mode 100644 index 00000000000..c21ce810e0d --- /dev/null +++ b/modules/nf-core/parabricks/deepvariant/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: 'PARABRICKS_DEEPVARIANT' { + ext.args = params.module_args + } + +} \ No newline at end of file diff --git a/modules/nf-core/parabricks/genotypegvcf/meta.yml b/modules/nf-core/parabricks/genotypegvcf/meta.yml index a876011edd0..a044fa88795 100644 --- a/modules/nf-core/parabricks/genotypegvcf/meta.yml +++ b/modules/nf-core/parabricks/genotypegvcf/meta.yml @@ -53,3 +53,5 @@ output: authors: - "@Furentsu" - "@bsiranosian" +maintainers: + - "@famosab" \ No newline at end of file diff --git a/modules/nf-core/parabricks/indexgvcf/meta.yml b/modules/nf-core/parabricks/indexgvcf/meta.yml index bc0e277660a..16834c645d6 100644 --- a/modules/nf-core/parabricks/indexgvcf/meta.yml +++ b/modules/nf-core/parabricks/indexgvcf/meta.yml @@ -44,3 +44,5 @@ output: authors: - "@Furentsu" - "@bsiranosian" +maintainers: + - "@famosab" \ No newline at end of file diff --git a/modules/nf-core/parabricks/mutectcaller/meta.yml b/modules/nf-core/parabricks/mutectcaller/meta.yml index baa6ab3e318..4e67686989a 100644 --- a/modules/nf-core/parabricks/mutectcaller/meta.yml +++ b/modules/nf-core/parabricks/mutectcaller/meta.yml @@ -90,3 +90,5 @@ output: pattern: "versions.yml" authors: - "@bsiranosian" +maintainers: + - "@famosab" \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 6eef66aaa8b..388211af598 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -347,9 +347,6 @@ ncbitools/vecscreen: oncocnv: - modules/nf-core/oncocnv/** - tests/modules/nf-core/oncocnv/** -parabricks/deepvariant: - - modules/nf-core/parabricks/deepvariant/** - - tests/modules/nf-core/parabricks/deepvariant/** parabricks/haplotypecaller: - modules/nf-core/parabricks/haplotypecaller/** - tests/modules/nf-core/parabricks/haplotypecaller/** diff --git a/tests/modules/nf-core/parabricks/deepvariant/main.nf b/tests/modules/nf-core/parabricks/deepvariant/main.nf deleted file mode 100644 index 9023189bbb9..00000000000 --- a/tests/modules/nf-core/parabricks/deepvariant/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PARABRICKS_DEEPVARIANT } from '../../../../../modules/nf-core/parabricks/deepvariant/main.nf' -include { PARABRICKS_DEEPVARIANT as PARABRICKS_DEEPVARIANT_GVCF } from '../../../../../modules/nf-core/parabricks/deepvariant/main.nf' - -workflow test_parabricks_deepvariant { - - input = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - [], // bam not needed unless using intervals - [] - ] - fasta = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - ] - - PARABRICKS_DEEPVARIANT ( input, fasta ) -} - -workflow test_parabricks_deepvariant_intervals { - - input = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) - ] - fasta = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - ] - - - PARABRICKS_DEEPVARIANT ( input, fasta ) -} - -workflow test_parabricks_deepvariant_gvcf { - - input = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true) - ] - fasta = [ - [ id:'test'], - file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) - ] - - PARABRICKS_DEEPVARIANT_GVCF ( input, fasta ) -} \ No newline at end of file diff --git a/tests/modules/nf-core/parabricks/deepvariant/nextflow.config b/tests/modules/nf-core/parabricks/deepvariant/nextflow.config deleted file mode 100644 index 9fbafc63d37..00000000000 --- a/tests/modules/nf-core/parabricks/deepvariant/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: PARABRICKS_DEEPVARIANT_GVCF { - ext.args = "--gvcf" - } -} diff --git a/tests/modules/nf-core/parabricks/deepvariant/test.yml b/tests/modules/nf-core/parabricks/deepvariant/test.yml deleted file mode 100644 index 9d1db86ba61..00000000000 --- a/tests/modules/nf-core/parabricks/deepvariant/test.yml +++ /dev/null @@ -1,29 +0,0 @@ -- name: parabricks deepvariant test_parabricks_deepvariant - command: nextflow run ./tests/modules/nf-core/parabricks/deepvariant -entry test_parabricks_deepvariant -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/deepvariant/nextflow.config -stub-run - tags: - - parabricks/deepvariant - - parabricks - files: - - path: output/parabricks/test.vcf - should_exist: true - - path: output/parabricks/versions.yml - -- name: parabricks deepvariant test_parabricks_deepvariant_intervals - command: nextflow run ./tests/modules/nf-core/parabricks/deepvariant -entry test_parabricks_deepvariant_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/deepvariant/nextflow.config -stub-run - tags: - - parabricks/deepvariant - - parabricks - files: - - path: output/parabricks/test.vcf - should_exist: true - - path: output/parabricks/versions.yml - -- name: parabricks deepvariant test_parabricks_deepvariant_gvcf - command: nextflow run ./tests/modules/nf-core/parabricks/deepvariant -entry test_parabricks_deepvariant_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/deepvariant/nextflow.config -stub-run - tags: - - parabricks/deepvariant - - parabricks - files: - - path: output/parabricks/test.g.vcf - should_exist: true - - path: output/parabricks/versions.yml diff --git a/tests/modules/nf-core/parabricks/deepvariant/test_GPU_config.txt b/tests/modules/nf-core/parabricks/deepvariant/test_GPU_config.txt deleted file mode 100644 index f64deb68675..00000000000 --- a/tests/modules/nf-core/parabricks/deepvariant/test_GPU_config.txt +++ /dev/null @@ -1,14 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - memory = "15.GB" - cpus = 4 - accelerator = 1 - - withName: PARABRICKS_DEEPVARIANT_GVCF { - ext.args = "--gvcf" - } -} - -docker.runOptions = "--gpus all" -singularity.runOptions = "--nv" diff --git a/tests/modules/nf-core/parabricks/deepvariant/test_GPU_yml.txt b/tests/modules/nf-core/parabricks/deepvariant/test_GPU_yml.txt deleted file mode 100644 index 8718ea4ceb8..00000000000 --- a/tests/modules/nf-core/parabricks/deepvariant/test_GPU_yml.txt +++ /dev/null @@ -1,29 +0,0 @@ -- name: parabricks deepvariant test_parabricks_deepvariant - command: nextflow run ./tests/modules/nf-core/parabricks/deepvariant -entry test_parabricks_deepvariant -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/deepvariant/nextflow.config - tags: - - parabricks/deepvariant - - parabricks - files: - - path: output/parabricks/test.vcf - should_exist: true - - path: output/parabricks/versions.yml - -- name: parabricks deepvariant test_parabricks_deepvariant_intervals - command: nextflow run ./tests/modules/nf-core/parabricks/deepvariant -entry test_parabricks_deepvariant_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/deepvariant/nextflow.config - tags: - - parabricks/deepvariant - - parabricks - files: - - path: output/parabricks/test.vcf - should_exist: true - - path: output/parabricks/versions.yml - -- name: parabricks deepvariant test_parabricks_deepvariant_gvcf - command: nextflow run ./tests/modules/nf-core/parabricks/deepvariant -entry test_parabricks_deepvariant_gvcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/deepvariant/nextflow.config - tags: - - parabricks/deepvariant - - parabricks - files: - - path: output/parabricks/test.g.vcf - should_exist: true - - path: output/parabricks/versions.yml