diff --git a/modules/nf-core/mlst/main.nf b/modules/nf-core/mlst/main.nf index 843d5d1adaa..4b204fc4324 100644 --- a/modules/nf-core/mlst/main.nf +++ b/modules/nf-core/mlst/main.nf @@ -2,10 +2,10 @@ process MLST { tag "$meta.id" label 'process_low' - conda "bioconda::mlst=2.19.0" + conda "bioconda::mlst=2.23.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : - 'biocontainers/mlst:2.19.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_0' : + 'biocontainers/mlst:2.23.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/mlst/meta.yml b/modules/nf-core/mlst/meta.yml index a5ac8ebd675..fe850351e5d 100644 --- a/modules/nf-core/mlst/meta.yml +++ b/modules/nf-core/mlst/meta.yml @@ -2,6 +2,10 @@ name: mlst description: Run Torsten Seemann's classic MLST on a genome assembly keywords: - mlst + - typing + - bacteria + - assembly + tools: - mlst: description: Scan contig files against PubMLST typing schemes diff --git a/modules/nf-core/mlst/tests/main.nf.test b/modules/nf-core/mlst/tests/main.nf.test new file mode 100644 index 00000000000..05744595891 --- /dev/null +++ b/modules/nf-core/mlst/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process MLST" + script "../main.nf" + process "MLST" + tag "mlst" + tag "modules" + tag "modules_nfcore" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file("https://raw.githubusercontent.com/nf-core/test-datasets/bactmap/genome/NCTC13799.fna", checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mlst/tests/main.nf.test.snap b/modules/nf-core/mlst/tests/main.nf.test.snap new file mode 100644 index 00000000000..1a33133783e --- /dev/null +++ b/modules/nf-core/mlst/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,b52df6178834a156c9402012718eb65e" + ] + ], + "1": [ + "versions.yml:md5,940bbbc3f20d9bee11bdf66fc910cc69" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,b52df6178834a156c9402012718eb65e" + ] + ], + "versions": [ + "versions.yml:md5,940bbbc3f20d9bee11bdf66fc910cc69" + ] + } + ], + "timestamp": "2023-10-18T03:41:42.858668172" + } +} \ No newline at end of file diff --git a/modules/nf-core/mlst/tests/tags.yml b/modules/nf-core/mlst/tests/tags.yml new file mode 100644 index 00000000000..1002abbfc06 --- /dev/null +++ b/modules/nf-core/mlst/tests/tags.yml @@ -0,0 +1,2 @@ +mlst: + - modules/nf-core/mlst/** diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index cc5d2fcbc3b..0742068a525 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -2461,10 +2461,6 @@ mitohifi/mitohifi: - modules/nf-core/mitohifi/mitohifi/** - tests/modules/nf-core/mitohifi/mitohifi/** -mlst: - - modules/nf-core/mlst/** - - tests/modules/nf-core/mlst/** - mmseqs/cluster: - modules/nf-core/mmseqs/cluster/** - tests/modules/nf-core/mmseqs/cluster/**