diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index c7c37084e52..52c5386d16c 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test @@ -35,8 +35,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) ] input[1] = UNTAR.out.untar println(projectDir) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 98f9adb18dd..330a1f3d964 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -8,7 +8,7 @@ process RTGTOOLS_VCFEVAL { 'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" input: - tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(evaluation_bed) + tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(regions_bed) tuple val(meta2), path(sdf) output: @@ -33,8 +33,8 @@ process RTGTOOLS_VCFEVAL { script: def args = task.ext.args ?: "" def prefix = task.ext.prefix ?: "${meta.id}" - def bed_regions = truth_bed ? "--bed-regions=${truth_bed}" : "" - def eval_regions = evaluation_bed ? "--evaluation-regions=${evaluation_bed}" : "" + def bed_regions = regions_bed ? "--bed-regions=${regions_bed}" : "" + def eval_regions = truth_bed ? "--evaluation-regions=${truth_bed}" : "" def truth_index = truth_vcf_tbi ? "" : "rtg index ${truth_vcf}" def query_index = query_vcf_tbi ? "" : "rtg index ${query_vcf}" def avail_mem = task.memory.toGiga() + "G" @@ -68,17 +68,17 @@ process RTGTOOLS_VCFEVAL { def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.tp.vcf.gz + echo | gzip > ${prefix}.tp.vcf.gz touch ${prefix}.tp.vcf.gz.tbi - touch ${prefix}.fn.vcf.gz + echo | gzip > ${prefix}.fn.vcf.gz touch ${prefix}.fn.vcf.gz.tbi - touch ${prefix}.fp.vcf.gz + echo | gzip > ${prefix}.fp.vcf.gz touch ${prefix}.fp.vcf.gz.tbi - touch ${prefix}.tp-baseline.vcf.gz + echo | gzip > ${prefix}.tp-baseline.vcf.gz touch ${prefix}.tp-baseline.vcf.gz.tbi - touch ${prefix}.snp_roc.tsv.gz - touch ${prefix}.non_snp_roc.tsv.gz - touch ${prefix}.weighted_roc.tsv.gz + echo | gzip > ${prefix}.snp_roc.tsv.gz + echo | gzip > ${prefix}.non_snp_roc.tsv.gz + echo | gzip > ${prefix}.weighted_roc.tsv.gz touch ${prefix}.summary.txt touch ${prefix}.phasing.txt diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index 9814124ee79..4c59bab5216 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -40,11 +40,13 @@ input: type: file description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) + This input should be used to provide the golden truth BED files. pattern: "*.bed" - - evaluation_bed: + - regions_bed: type: file description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) + This input should be used to provide the regions used by the analysis pattern: "*.bed" - - meta2: type: map diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test new file mode 100644 index 00000000000..55abc842759 --- /dev/null +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test @@ -0,0 +1,113 @@ +nextflow_process { + + name "Test Process RTGTOOLS_VCFEVAL" + script "../main.nf" + process "RTGTOOLS_VCFEVAL" + + tag "modules" + tag "modules_nfcore" + tag "rtgtools" + tag "rtgtools/vcfeval" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.value([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz', checkIfExists:true) + ]) + """ + } + } + } + + test("homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf") { + + when { + process { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists:true) + ]) + input[1] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, [], truth, [], [], []], sdf") { + + when { + process { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), + [], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true), + [], + [], + [] + ]) + input[1] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists:true) + ]) + input[1] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap new file mode 100644 index 00000000000..4f39e2d4641 --- /dev/null +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap @@ -0,0 +1,677 @@ +{ + "homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "10": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + ] + ], + "11": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,f4c8df93c8bdab603036bbc27b4a28c3" + ] + ], + "12": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,31988234bee208cacb3de90dabe1797f" + ] + ], + "13": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "2": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "6": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + ] + ], + "baseline_tbi": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "baseline_vcf": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "fn_tbi": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "fn_vcf": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "fp_tbi": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "fp_vcf": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "non_snp_roc": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + ] + ], + "phasing": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,31988234bee208cacb3de90dabe1797f" + ] + ], + "snp_roc": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,f4c8df93c8bdab603036bbc27b4a28c3" + ] + ], + "tp_tbi": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "tp_vcf": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "versions": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "weighted_roc": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:17:31.564974666" + }, + "homo_sapiens - 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[vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "11": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "13": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "2": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "baseline_tbi": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "baseline_vcf": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "fn_tbi": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fn_vcf": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "fp_tbi": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fp_vcf": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "non_snp_roc": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "phasing": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "snp_roc": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tp_tbi": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tp_vcf": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "weighted_roc": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:23:21.165461388" + } +} \ No newline at end of file diff --git a/modules/nf-core/rtgtools/vcfeval/tests/nextflow.config b/modules/nf-core/rtgtools/vcfeval/tests/nextflow.config new file mode 100644 index 00000000000..7563521514f --- /dev/null +++ b/modules/nf-core/rtgtools/vcfeval/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + withName: UNTAR { + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index c5ede631186..485641f1da0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -578,9 +578,6 @@ roary: rtgtools/format: - modules/nf-core/rtgtools/format/** - tests/modules/nf-core/rtgtools/format/** -rtgtools/vcfeval: - - modules/nf-core/rtgtools/vcfeval/** - - tests/modules/nf-core/rtgtools/vcfeval/** scramble/clusteranalysis: - modules/nf-core/scramble/clusteranalysis/** - tests/modules/nf-core/scramble/clusteranalysis/** diff --git a/tests/modules/nf-core/rtgtools/vcfeval/main.nf b/tests/modules/nf-core/rtgtools/vcfeval/main.nf deleted file mode 100644 index 7ca921fcaed..00000000000 --- a/tests/modules/nf-core/rtgtools/vcfeval/main.nf +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { RTGTOOLS_VCFEVAL } from '../../../../../modules/nf-core/rtgtools/vcfeval/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' - -workflow test_rtgtools_vcfeval { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) - ] - - compressed_sdf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) - ] - - sdf = UNTAR( compressed_sdf ).untar - - RTGTOOLS_VCFEVAL ( input, sdf ) -} - -workflow test_rtgtools_vcfeval_no_optional_inputs { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - [], - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - [], - [], - [] - ] - - compressed_sdf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) - ] - - sdf = UNTAR( compressed_sdf ).untar - - RTGTOOLS_VCFEVAL ( input, sdf ) -} diff --git a/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config b/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config deleted file mode 100644 index 4ced2e3b2ab..00000000000 --- a/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: UNTAR { - publishDir = [enabled:false] - } -} diff --git a/tests/modules/nf-core/rtgtools/vcfeval/test.yml b/tests/modules/nf-core/rtgtools/vcfeval/test.yml deleted file mode 100644 index 8f89d2b44b6..00000000000 --- a/tests/modules/nf-core/rtgtools/vcfeval/test.yml +++ /dev/null @@ -1,67 +0,0 @@ -- name: rtgtools vcfeval test_rtgtools_vcfeval - command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rtgtools/vcfeval/nextflow.config - tags: - - rtgtools/vcfeval - - rtgtools - files: - - path: output/rtgtools/test.fn.vcf.gz - md5sum: 65142f7398361eebb00028255c4645f9 - - path: output/rtgtools/test.fn.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.fp.vcf.gz - md5sum: 459988c1aa5206214587044971db2518 - - path: output/rtgtools/test.fp.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.non_snp_roc.tsv.gz - md5sum: 0ccf995d071c7d27812e9e899b67050a - - path: output/rtgtools/test.phasing.txt - md5sum: 31988234bee208cacb3de90dabe1797f - - path: output/rtgtools/test.snp_roc.tsv.gz - md5sum: cff421e8b15db7d92355fbef0be5ec93 - - path: output/rtgtools/test.summary.txt - md5sum: f4c8df93c8bdab603036bbc27b4a28c3 - - path: output/rtgtools/test.tp-baseline.vcf.gz - md5sum: 65142f7398361eebb00028255c4645f9 - - path: output/rtgtools/test.tp-baseline.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.tp.vcf.gz - md5sum: 459988c1aa5206214587044971db2518 - - path: output/rtgtools/test.tp.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.weighted_roc.tsv.gz - md5sum: 946dd5b0a6f33993bc2f7378c503c5cc - - path: output/rtgtools/versions.yml - -- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs - command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rtgtools/vcfeval/nextflow.config - tags: - - rtgtools/vcfeval - - rtgtools - files: - - path: output/rtgtools/test.fn.vcf.gz - md5sum: 6a148698fa6c20d6e5bbe384d962363a - - path: output/rtgtools/test.fn.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.fp.vcf.gz - md5sum: 9c1606449d3c256233bdd2b6c8016776 - - path: output/rtgtools/test.fp.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.non_snp_roc.tsv.gz - md5sum: 9990107a5d8951e124d452f6cac26062 - - path: output/rtgtools/test.phasing.txt - md5sum: 133677dbd8be657439ea2b03fdfb8795 - - path: output/rtgtools/test.snp_roc.tsv.gz - md5sum: cde86d34fa86475194e29a74dfc9090c - - path: output/rtgtools/test.summary.txt - md5sum: f33feb32f84958fb931063044fba369b - - path: output/rtgtools/test.tp-baseline.vcf.gz - md5sum: 5d9bb9b55b03d42c1726c0c32498b624 - - path: output/rtgtools/test.tp-baseline.vcf.gz.tbi - md5sum: 95938320b425e28cf06c45ab45ad0360 - - path: output/rtgtools/test.tp.vcf.gz - md5sum: d771fa4d28b42b43e698cee93c92cf65 - - path: output/rtgtools/test.tp.vcf.gz.tbi - md5sum: a0e9ac2d38c04bd591ab8f857c5c9133 - - path: output/rtgtools/test.weighted_roc.tsv.gz - md5sum: 005c2e8bacaaab0b409da449301d67fd - - path: output/rtgtools/versions.yml