diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test new file mode 100644 index 00000000000..0f65f542891 --- /dev/null +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test @@ -0,0 +1,44 @@ + +nextflow_process { + + name "Test Process GATK4_CONDENSEDEPTHEVIDENCE" + script "../main.nf" + process "GATK4_CONDENSEDEPTHEVIDENCE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/condensedepthevidence" + + test("test-gatk4-condensdepthevidence") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.condensed_evidence[0][1]).linesGzip[0..1], + file(process.out.condensed_evidence_index[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap new file mode 100644 index 00000000000..d8da0978b2b --- /dev/null +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "test-gatk4-condensdepthevidence": { + "content": [ + [ + "#Chr\tStart\tEnd\ttestN", + "chr22\t0\t40001\t5642" + ], + "test.rd.txt.gz.tbi", + [ + "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:33:21.910858" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 0e4669b6ca6..55568e89ef3 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -386,9 +386,6 @@ gatk4/cnnscorevariants: gatk4/collectsvevidence: - modules/nf-core/gatk4/collectsvevidence/** - tests/modules/nf-core/gatk4/collectsvevidence/** -gatk4/condensedepthevidence: - - modules/nf-core/gatk4/condensedepthevidence/** - - tests/modules/nf-core/gatk4/condensedepthevidence/** gatk4/createreadcountpanelofnormals: - modules/nf-core/gatk4/createreadcountpanelofnormals/** - tests/modules/nf-core/gatk4/createreadcountpanelofnormals/** diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf b/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf deleted file mode 100644 index dc3c89640f7..00000000000 --- a/tests/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GATK4_CONDENSEDEPTHEVIDENCE } from '../../../../../modules/nf-core/gatk4/condensedepthevidence/main.nf' - -workflow test_gatk4_condensdepthevidence { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), - file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true) - ] - - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - - GATK4_CONDENSEDEPTHEVIDENCE ( - input, - fasta, - fasta_fai, - dict - ) -} diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config b/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config deleted file mode 100644 index 8730f1c4b93..00000000000 --- a/tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml b/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml deleted file mode 100644 index 671d81dcab0..00000000000 --- a/tests/modules/nf-core/gatk4/condensedepthevidence/test.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: gatk4 condensedepthevidence test_gatk4_condensdepthevidence - command: nextflow run ./tests/modules/nf-core/gatk4/condensedepthevidence -entry test_gatk4_condensdepthevidence -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gatk4/condensedepthevidence/nextflow.config - tags: - - gatk4 - - gatk4/condensedepthevidence - files: - - path: output/gatk4/test.rd.txt.gz - md5sum: c6c04b78f2aa40744f267518b3cb21b8 - - path: output/gatk4/test.rd.txt.gz.tbi - md5sum: c30d5548ad94063b105e227483b68779 - - path: output/gatk4/versions.yml