From c299a12e25c5ceb0cf6de5aa71a620b9dbe6c909 Mon Sep 17 00:00:00 2001 From: LouisLeNezet Date: Sun, 23 Mar 2025 19:29:46 +0100 Subject: [PATCH] Migrate to nf-test --- modules/nf-core/ataqv/mkarv/main.nf | 11 ++ .../nf-core/ataqv/mkarv/tests/main.nf.test | 79 +++++++++++ .../ataqv/mkarv/tests/main.nf.test.snap | 123 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/ataqv/mkarv/main.nf | 19 --- .../nf-core/ataqv/mkarv/nextflow.config | 5 - tests/modules/nf-core/ataqv/mkarv/test.yml | 55 -------- 7 files changed, 213 insertions(+), 82 deletions(-) create mode 100644 modules/nf-core/ataqv/mkarv/tests/main.nf.test create mode 100644 modules/nf-core/ataqv/mkarv/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/ataqv/mkarv/main.nf delete mode 100644 tests/modules/nf-core/ataqv/mkarv/nextflow.config delete mode 100644 tests/modules/nf-core/ataqv/mkarv/test.yml diff --git a/modules/nf-core/ataqv/mkarv/main.nf b/modules/nf-core/ataqv/mkarv/main.nf index 9f45c77fe640..ade0b50cd218 100644 --- a/modules/nf-core/ataqv/mkarv/main.nf +++ b/modules/nf-core/ataqv/mkarv/main.nf @@ -32,4 +32,15 @@ process ATAQV_MKARV { ataqv: \$( ataqv --version ) END_VERSIONS """ + + stub: + """ + mkdir -p html + touch html/index.html + cat <<-END_VERSIONS > versions.yml + "${task.process}": + # mkarv: \$( mkarv --version ) # Use this when version string has been fixed + ataqv: \$( ataqv --version ) + END_VERSIONS + """ } diff --git a/modules/nf-core/ataqv/mkarv/tests/main.nf.test b/modules/nf-core/ataqv/mkarv/tests/main.nf.test new file mode 100644 index 000000000000..c2b5bbe89022 --- /dev/null +++ b/modules/nf-core/ataqv/mkarv/tests/main.nf.test @@ -0,0 +1,79 @@ +nextflow_process { + + name "Test Process ATAQV_MKARV" + + script "../main.nf" + process "ATAQV_MKARV" + + tag "modules" + tag "modules_nfcore" + tag "ataqv" + tag "ataqv/ataqv" + tag "ataqv/mkarv" + + setup { + run("ATAQV_ATAQV") { + script "../../ataqv/main.nf" + + process { + """ + input[0] = [ + [id:'test',single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam',checkIfExists:true), + [], + [] + ] + input[1] = 'human' + input[2] = '' + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + } + + test("test_ataqv_mkarv") { + when { + params { + module_args = '' + } + process { + """ + input[0] = ATAQV_ATAQV.out.json.collect{it[1]} + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_ataqv_mkarv - stub") { + + options '-stub' + + when { + params { + module_args = '' + } + process { + """ + input[0] = ATAQV_ATAQV.out.json.collect{it[1]} + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + process.out.versions.collect{path(it).yaml} + ).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/ataqv/mkarv/tests/main.nf.test.snap b/modules/nf-core/ataqv/mkarv/tests/main.nf.test.snap new file mode 100644 index 000000000000..86057ae88a06 --- /dev/null +++ b/modules/nf-core/ataqv/mkarv/tests/main.nf.test.snap @@ -0,0 +1,123 @@ +{ + "test_ataqv_mkarv - stub": { + "content": [ + { + "0": [ + [ + "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f" + ], + "html": [ + [ + "index.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f" + ] + }, + [ + { + "ATAQV_MKARV": { + "ataqv": "1.3.1" + } + } + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-23T19:29:21.09850825" + }, + "test_ataqv_mkarv": { + "content": [ + { + "0": [ + [ + [ + "ataqv.css:md5,7bb9e18974018dd29bdc12a46a6d6d65", + "datatables.buttons.min.css:md5,675306abc9d3239314f2c66c0e22ef7a", + "datatables.fontawesome.css:md5,716d7a3edd2c75e712b1ffe26f12a861", + "datatables.min.css:md5,00ef3e39d9302618395ab189ec8bcd9f", + "font-awesome.min.css:md5,89916fa773ce96569604016ef25cab50", + "normalize.css:md5,40d20cc85100840580df4346bb99d7ed" + ], + [ + "1.json.gz:md5,7c01e4f0136404e6db2328485d68d154" + ], + [ + "FontAwesome.otf:md5,9ccfa32dd4cd1b8e83f68899d85bd5e6", + "fontawesome-webfont.eot:md5,404a525502f8e5ba7e93b9f02d9e83a9", + "fontawesome-webfont.svg:md5,bae4a87c1e5dff40baa3f49d52f5347a", + "fontawesome-webfont.ttf:md5,fb650aaf10736ffb9c4173079616bf01", + "fontawesome-webfont.woff:md5,891e3f340c1126b4c7c142e5f6e86816", + "fontawesome-webfont.woff2:md5,926c93d201fe51c8f351e858468980c3", + "sourcesanspro-regular.woff:md5,f7bd788f18b8c4bb93dd37d140348e1e", + "sourcesanspro-regularit.woff:md5,c3638b17f4fd76dae12fe2ae14571e57", + "sourcesanspro-semibold.woff:md5,e7fc8925d9364e9d177d9e1d08bb1855", + "sourcesanspro-semiboldit.woff:md5,f1d255aa459786dfc6aa2e488ac01245" + ], + "index.html:md5,bf7747be761e56ad7c54c842ac88461a", + [ + "ataqv.js:md5,feb291b7839e9e43ed304565e3a605d9", + "configuration.js:md5,073bc07f1371e28a97098f8b10469ae4", + "d3.min.js:md5,db69fb2626a71a286ee772d673138aca", + "datatables.min.js:md5,e369b872620dadb05e4eb555b81f9112", + "jszip.min.js:md5,09e492cb492ffa75484bbe10f1f721d1" + ] + ] + ], + "1": [ + "versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f" + ], + "html": [ + [ + [ + "ataqv.css:md5,7bb9e18974018dd29bdc12a46a6d6d65", + "datatables.buttons.min.css:md5,675306abc9d3239314f2c66c0e22ef7a", + "datatables.fontawesome.css:md5,716d7a3edd2c75e712b1ffe26f12a861", + "datatables.min.css:md5,00ef3e39d9302618395ab189ec8bcd9f", + "font-awesome.min.css:md5,89916fa773ce96569604016ef25cab50", + "normalize.css:md5,40d20cc85100840580df4346bb99d7ed" + ], + [ + "1.json.gz:md5,7c01e4f0136404e6db2328485d68d154" + ], + [ + "FontAwesome.otf:md5,9ccfa32dd4cd1b8e83f68899d85bd5e6", + "fontawesome-webfont.eot:md5,404a525502f8e5ba7e93b9f02d9e83a9", + "fontawesome-webfont.svg:md5,bae4a87c1e5dff40baa3f49d52f5347a", + "fontawesome-webfont.ttf:md5,fb650aaf10736ffb9c4173079616bf01", + "fontawesome-webfont.woff:md5,891e3f340c1126b4c7c142e5f6e86816", + "fontawesome-webfont.woff2:md5,926c93d201fe51c8f351e858468980c3", + "sourcesanspro-regular.woff:md5,f7bd788f18b8c4bb93dd37d140348e1e", + "sourcesanspro-regularit.woff:md5,c3638b17f4fd76dae12fe2ae14571e57", + "sourcesanspro-semibold.woff:md5,e7fc8925d9364e9d177d9e1d08bb1855", + "sourcesanspro-semiboldit.woff:md5,f1d255aa459786dfc6aa2e488ac01245" + ], + "index.html:md5,bf7747be761e56ad7c54c842ac88461a", + [ + "ataqv.js:md5,feb291b7839e9e43ed304565e3a605d9", + "configuration.js:md5,073bc07f1371e28a97098f8b10469ae4", + "d3.min.js:md5,db69fb2626a71a286ee772d673138aca", + "datatables.min.js:md5,e369b872620dadb05e4eb555b81f9112", + "jszip.min.js:md5,09e492cb492ffa75484bbe10f1f721d1" + ] + ] + ], + "versions": [ + "versions.yml:md5,f0f11bfec7e5fc5776c4af08db94655f" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-23T19:24:40.06356836" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 340e2b637b12..4bafcd29c484 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,6 +1,3 @@ -ataqv/mkarv: - - modules/nf-core/ataqv/mkarv/** - - tests/modules/nf-core/ataqv/mkarv/** authentict/deam2cont: - modules/nf-core/authentict/deam2cont/** - tests/modules/nf-core/authentict/deam2cont/** diff --git a/tests/modules/nf-core/ataqv/mkarv/main.nf b/tests/modules/nf-core/ataqv/mkarv/main.nf deleted file mode 100644 index 33c4334ee606..000000000000 --- a/tests/modules/nf-core/ataqv/mkarv/main.nf +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ATAQV_ATAQV } from '../../../../../modules/nf-core/ataqv/ataqv/main.nf' -include { ATAQV_MKARV } from '../../../../../modules/nf-core/ataqv/mkarv/main.nf' - -workflow test_ataqv_mkarv { - - input = [ - [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), - [], - [] - ] - - ATAQV_ATAQV ( input, 'human', '', [], [], [] ) - ATAQV_MKARV ( ATAQV_ATAQV.out.json.collect{ it[1]} ) -} diff --git a/tests/modules/nf-core/ataqv/mkarv/nextflow.config b/tests/modules/nf-core/ataqv/mkarv/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/ataqv/mkarv/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/ataqv/mkarv/test.yml b/tests/modules/nf-core/ataqv/mkarv/test.yml deleted file mode 100644 index 184fac699e6e..000000000000 --- a/tests/modules/nf-core/ataqv/mkarv/test.yml +++ /dev/null @@ -1,55 +0,0 @@ -- name: ataqv mkarv test_ataqv_mkarv - command: nextflow run ./tests/modules/nf-core/ataqv/mkarv -entry test_ataqv_mkarv -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ataqv/mkarv/nextflow.config - tags: - - ataqv/mkarv - - ataqv - - files: - - path: output/ataqv/html/css/ataqv.css - md5sum: 7bb9e18974018dd29bdc12a46a6d6d65 - - path: output/ataqv/html/css/datatables.buttons.min.css - md5sum: 675306abc9d3239314f2c66c0e22ef7a - - path: output/ataqv/html/css/datatables.fontawesome.css - md5sum: 716d7a3edd2c75e712b1ffe26f12a861 - - path: output/ataqv/html/css/datatables.min.css - md5sum: 00ef3e39d9302618395ab189ec8bcd9f - - path: output/ataqv/html/css/font-awesome.min.css - md5sum: 89916fa773ce96569604016ef25cab50 - - path: output/ataqv/html/css/normalize.css - md5sum: 40d20cc85100840580df4346bb99d7ed - - path: output/ataqv/html/data/1.json.gz - - path: output/ataqv/html/fonts/FontAwesome.otf - md5sum: 9ccfa32dd4cd1b8e83f68899d85bd5e6 - - path: output/ataqv/html/fonts/fontawesome-webfont.eot - md5sum: 404a525502f8e5ba7e93b9f02d9e83a9 - - path: output/ataqv/html/fonts/fontawesome-webfont.svg - md5sum: bae4a87c1e5dff40baa3f49d52f5347a - - path: output/ataqv/html/fonts/fontawesome-webfont.ttf - md5sum: fb650aaf10736ffb9c4173079616bf01 - - path: output/ataqv/html/fonts/fontawesome-webfont.woff - md5sum: 891e3f340c1126b4c7c142e5f6e86816 - - path: output/ataqv/html/fonts/fontawesome-webfont.woff2 - md5sum: 926c93d201fe51c8f351e858468980c3 - - path: output/ataqv/html/fonts/sourcesanspro-regular.woff - md5sum: f7bd788f18b8c4bb93dd37d140348e1e - - path: output/ataqv/html/fonts/sourcesanspro-regularit.woff - md5sum: c3638b17f4fd76dae12fe2ae14571e57 - - path: output/ataqv/html/fonts/sourcesanspro-semibold.woff - md5sum: e7fc8925d9364e9d177d9e1d08bb1855 - - path: output/ataqv/html/fonts/sourcesanspro-semiboldit.woff - md5sum: f1d255aa459786dfc6aa2e488ac01245 - - path: output/ataqv/html/index.html - md5sum: bf7747be761e56ad7c54c842ac88461a - - path: output/ataqv/html/js/ataqv.js - md5sum: feb291b7839e9e43ed304565e3a605d9 - - path: output/ataqv/html/js/configuration.js - md5sum: 073bc07f1371e28a97098f8b10469ae4 - - path: output/ataqv/html/js/d3.min.js - md5sum: db69fb2626a71a286ee772d673138aca - - path: output/ataqv/html/js/datatables.min.js - md5sum: e369b872620dadb05e4eb555b81f9112 - - path: output/ataqv/html/js/jszip.min.js - md5sum: 09e492cb492ffa75484bbe10f1f721d1 - - path: output/ataqv/test.ataqv.json - contains: - - '"properly_paired_and_mapped_reads": 192,'