diff --git a/modules/nf-core/legsta/environment.yml b/modules/nf-core/legsta/environment.yml index 34d11fcfbe3..ae157ec4a90 100644 --- a/modules/nf-core/legsta/environment.yml +++ b/modules/nf-core/legsta/environment.yml @@ -2,6 +2,5 @@ name: legsta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::legsta=0.5.1 diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index d28d01bbb3e..d776d64153f 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -30,4 +30,15 @@ process LEGSTA { legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;') + END_VERSIONS + """ } diff --git a/modules/nf-core/legsta/meta.yml b/modules/nf-core/legsta/meta.yml index 39943833239..734498e0612 100644 --- a/modules/nf-core/legsta/meta.yml +++ b/modules/nf-core/legsta/meta.yml @@ -3,6 +3,8 @@ description: Typing of clinical and environmental isolates of Legionella pneumop keywords: - bacteria - legionella + - clinical + - pneumophila tools: - legsta: description: In silico Legionella pneumophila Sequence Based Typing diff --git a/modules/nf-core/legsta/tests/main.nf.test b/modules/nf-core/legsta/tests/main.nf.test new file mode 100644 index 00000000000..bed639db0a6 --- /dev/null +++ b/modules/nf-core/legsta/tests/main.nf.test @@ -0,0 +1,57 @@ + +nextflow_process { + + name "Test Process LEGSTA" + script "../main.nf" + process "LEGSTA" + + tag "modules" + tag "modules_nfcore" + tag "legsta" + + test("test-legsta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-legsta-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/legsta/tests/main.nf.test.snap b/modules/nf-core/legsta/tests/main.nf.test.snap new file mode 100644 index 00000000000..54adc1906f7 --- /dev/null +++ b/modules/nf-core/legsta/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-legsta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8" + ] + ], + "1": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8" + ] + ], + "versions": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:09:21.017956" + }, + "test-legsta-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:09:26.594828" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 57288b26ea9..db4bb9e89d3 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -434,9 +434,6 @@ krona/ktupdatetaxonomy: leehom: - modules/nf-core/leehom/** - tests/modules/nf-core/leehom/** -legsta: - - modules/nf-core/legsta/** - - tests/modules/nf-core/legsta/** limma/differential: - modules/nf-core/limma/differential/** - tests/modules/nf-core/limma/differential/** diff --git a/tests/modules/nf-core/legsta/main.nf b/tests/modules/nf-core/legsta/main.nf deleted file mode 100644 index b74a9cf278a..00000000000 --- a/tests/modules/nf-core/legsta/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { LEGSTA } from '../../../../modules/nf-core/legsta/main.nf' - -workflow test_legsta { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - LEGSTA ( input ) -} diff --git a/tests/modules/nf-core/legsta/nextflow.config b/tests/modules/nf-core/legsta/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/legsta/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/legsta/test.yml b/tests/modules/nf-core/legsta/test.yml deleted file mode 100644 index 6d193422d34..00000000000 --- a/tests/modules/nf-core/legsta/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: legsta test_legsta - command: nextflow run ./tests/modules/nf-core/legsta -entry test_legsta -c ./tests/config/nextflow.config - tags: - - legsta - files: - - path: output/legsta/test.tsv - md5sum: c493bdd19335de4828aa8b4e3ce7e1f8 - - path: output/legsta/versions.yml - md5sum: d16c5f6fd68d2bcc2c71954e3342aabe