From c63d090f2eab760332163455f651a55ebd11b1de Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 26 Aug 2024 23:33:16 +1200 Subject: [PATCH] Added nf-test for bedtools/multiinter (#6327) --- .../bedtools/multiinter/tests/main.nf.test | 65 +++++++++++++++++ .../multiinter/tests/main.nf.test.snap | 72 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - .../nf-core/bedtools/multiinter/main.nf | 32 --------- .../bedtools/multiinter/nextflow.config | 5 -- .../nf-core/bedtools/multiinter/test.yml | 19 ----- 6 files changed, 137 insertions(+), 59 deletions(-) create mode 100644 modules/nf-core/bedtools/multiinter/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/bedtools/multiinter/main.nf delete mode 100644 tests/modules/nf-core/bedtools/multiinter/nextflow.config delete mode 100644 tests/modules/nf-core/bedtools/multiinter/test.yml diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test b/modules/nf-core/bedtools/multiinter/tests/main.nf.test new file mode 100644 index 00000000000..ed46cf0d3bc --- /dev/null +++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test @@ -0,0 +1,65 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_MULTIINTER" + script "../main.nf" + process "BEDTOOLS_MULTIINTER" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/multiinter" + + test("test-bedtools-multiinter") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true) + ] + ] + input[1] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-multiinter-genome") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true) + ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap b/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap new file mode 100644 index 00000000000..14cad906c41 --- /dev/null +++ b/modules/nf-core/bedtools/multiinter/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-bedtools-multiinter": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "1": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "versions": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:55:57.797405" + }, + "test-bedtools-multiinter-genome": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "1": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,03d8d889a19cf26e038868775bbcbaa7" + ] + ], + "versions": [ + "versions.yml:md5,d50d8662e6ba7227f29713a252d0b51c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:56:02.192345" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index bbec5c3f959..59735518afd 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -76,9 +76,6 @@ bedtools/makewindows: bedtools/maskfasta: - modules/nf-core/bedtools/maskfasta/** - tests/modules/nf-core/bedtools/maskfasta/** -bedtools/multiinter: - - modules/nf-core/bedtools/multiinter/** - - tests/modules/nf-core/bedtools/multiinter/** bedtools/shift: - modules/nf-core/bedtools/shift/** - tests/modules/nf-core/bedtools/shift/** diff --git a/tests/modules/nf-core/bedtools/multiinter/main.nf b/tests/modules/nf-core/bedtools/multiinter/main.nf deleted file mode 100644 index b453116857c..00000000000 --- a/tests/modules/nf-core/bedtools/multiinter/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_MULTIINTER } from '../../../../../modules/nf-core/bedtools/multiinter/main.nf' - -workflow test_bedtools_multiinter { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true) - ] - ] - - BEDTOOLS_MULTIINTER ( input, [] ) -} - -workflow test_bedtools_multiinter_genome { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true) - ] - ] - sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) - - BEDTOOLS_MULTIINTER ( input, sizes ) -} diff --git a/tests/modules/nf-core/bedtools/multiinter/nextflow.config b/tests/modules/nf-core/bedtools/multiinter/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/bedtools/multiinter/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/bedtools/multiinter/test.yml b/tests/modules/nf-core/bedtools/multiinter/test.yml deleted file mode 100644 index 16e7bca6636..00000000000 --- a/tests/modules/nf-core/bedtools/multiinter/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: bedtools multiinter test_bedtools_multiinter - command: nextflow run ./tests/modules/nf-core/bedtools/multiinter -entry test_bedtools_multiinter -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/multiinter/nextflow.config - tags: - - bedtools/multiinter - - bedtools - files: - - path: output/bedtools/test.bed - md5sum: 03d8d889a19cf26e038868775bbcbaa7 - - path: output/bedtools/versions.yml - -- name: bedtools multiinter test_bedtools_multiinter_genome - command: nextflow run ./tests/modules/nf-core/bedtools/multiinter -entry test_bedtools_multiinter_genome -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/multiinter/nextflow.config - tags: - - bedtools/multiinter - - bedtools - files: - - path: output/bedtools/test.bed - md5sum: 03d8d889a19cf26e038868775bbcbaa7 - - path: output/bedtools/versions.yml