diff --git a/modules/nf-core/tiara/tiara/meta.yml b/modules/nf-core/tiara/tiara/meta.yml index 5e532c0eca1..e9d6b0553d7 100644 --- a/modules/nf-core/tiara/tiara/meta.yml +++ b/modules/nf-core/tiara/tiara/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://ibe-uw.github.io/tiara/" tool_dev_url: "https://github.com/ibe-uw/tiara" doi: "10.1093/bioinformatics/btab672" - licence: "MIT" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/tiara/tiara/tests/main.nf.test b/modules/nf-core/tiara/tiara/tests/main.nf.test new file mode 100644 index 00000000000..8a926a56d17 --- /dev/null +++ b/modules/nf-core/tiara/tiara/tests/main.nf.test @@ -0,0 +1,42 @@ + +nextflow_process { + + name "Test Process TIARA_TIARA" + script "../main.nf" + process "TIARA_TIARA" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "tiara" + tag "tiara/tiara" + + test("illumina-contigs-fa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.classifications, + file(process.out.log[0][1]).name, + process.out.fasta, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/tiara/tiara/tests/main.nf.test.snap b/modules/nf-core/tiara/tiara/tests/main.nf.test.snap new file mode 100644 index 00000000000..2e259fa884b --- /dev/null +++ b/modules/nf-core/tiara/tiara/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "test-tiara-tiara": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,1e4a4d8081c20b2540316fb9fafb5ad3" + ] + ], + "log_test.txt", + [ + + ], + [ + "versions.yml:md5,4eeba8074325fb450c1cddd731431cc4" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T09:49:05.091671" + } +} \ No newline at end of file diff --git a/modules/nf-core/tiara/tiara/tests/nextflow.config b/modules/nf-core/tiara/tiara/tests/nextflow.config new file mode 100644 index 00000000000..dee2d0e43c9 --- /dev/null +++ b/modules/nf-core/tiara/tiara/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: TIARA_TIARA { + ext.args = "--tf bac" + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 102b215f7ee..9b868dc73f7 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1542,9 +1542,6 @@ tailfindr: tbprofiler/profile: - modules/nf-core/tbprofiler/profile/** - tests/modules/nf-core/tbprofiler/profile/** -tiara/tiara: - - modules/nf-core/tiara/tiara/** - - tests/modules/nf-core/tiara/tiara/** topas/gencons: - modules/nf-core/topas/gencons/** - tests/modules/nf-core/topas/gencons/** diff --git a/tests/modules/nf-core/tiara/tiara/main.nf b/tests/modules/nf-core/tiara/tiara/main.nf deleted file mode 100644 index 48cd4b49eb0..00000000000 --- a/tests/modules/nf-core/tiara/tiara/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { TIARA_TIARA } from '../../../../../modules/nf-core/tiara/tiara/main.nf' - -workflow test_tiara_tiara { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) - ] - - TIARA_TIARA ( input ) -} diff --git a/tests/modules/nf-core/tiara/tiara/nextflow.config b/tests/modules/nf-core/tiara/tiara/nextflow.config deleted file mode 100644 index 3232fb04d45..00000000000 --- a/tests/modules/nf-core/tiara/tiara/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: "test_tiara_tiara:TIARA_TIARA" { - ext.args = "--tf bac" - } - -} diff --git a/tests/modules/nf-core/tiara/tiara/test.yml b/tests/modules/nf-core/tiara/tiara/test.yml deleted file mode 100644 index 4c524483516..00000000000 --- a/tests/modules/nf-core/tiara/tiara/test.yml +++ /dev/null @@ -1,16 +0,0 @@ -- name: tiara tiara test_tiara_tiara - command: nextflow run ./tests/modules/nf-core/tiara/tiara -entry test_tiara_tiara -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/tiara/tiara/nextflow.config - tags: - - tiara - - tiara/tiara - files: - - path: output/tiara/bacteria_test.fasta - md5sum: d46834f0b781bc0277269f79226f5001 - - path: output/tiara/log_test.txt - contains: - - "hidden_1: 2048" - - "hidden_2: 1024" - - "prob_cutoff: 0.65" - - path: output/tiara/test.txt - md5sum: 1e4a4d8081c20b2540316fb9fafb5ad3 - - path: output/tiara/versions.yml