diff --git a/modules/nf-core/spring/compress/meta.yml b/modules/nf-core/spring/compress/meta.yml index f1958dc57ed..8b52160940c 100644 --- a/modules/nf-core/spring/compress/meta.yml +++ b/modules/nf-core/spring/compress/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md" tool_dev_url: "https://github.com/shubhamchandak94/Spring" doi: "10.1093/bioinformatics/bty1015" - licence: "['Free for non-commercial use']" + licence: ["Free for non-commercial use"] input: - meta: type: map diff --git a/modules/nf-core/spring/compress/tests/main.nf.test b/modules/nf-core/spring/compress/tests/main.nf.test new file mode 100644 index 00000000000..45690c34fd6 --- /dev/null +++ b/modules/nf-core/spring/compress/tests/main.nf.test @@ -0,0 +1,67 @@ + +nextflow_process { + + name "Test Process SPRING_COMPRESS" + script "../main.nf" + process "SPRING_COMPRESS" + + tag "modules" + tag "modules_nfcore" + tag "spring" + tag "spring/compress" + + test("test-spring-compress-single-end") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + [] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.spring[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-spring-compress-paired-end") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.spring[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/spring/compress/tests/main.nf.test.snap b/modules/nf-core/spring/compress/tests/main.nf.test.snap new file mode 100644 index 00000000000..c3a8912b2ee --- /dev/null +++ b/modules/nf-core/spring/compress/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "test-spring-compress-single-end": { + "content": [ + "test.spring", + [ + "versions.yml:md5,2882bc3a3593cb048417c38e7452a788" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-27T12:27:30.458355" + }, + "test-spring-compress-paired-end": { + "content": [ + "test.spring", + [ + "versions.yml:md5,2882bc3a3593cb048417c38e7452a788" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-27T12:27:35.271383" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 8384aafa635..a40bacaf4de 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1164,9 +1164,6 @@ sourmash/taxannotate: spatyper: - modules/nf-core/spatyper/** - tests/modules/nf-core/spatyper/** -spring/compress: - - modules/nf-core/spring/compress/** - - tests/modules/nf-core/spring/compress/** spring/decompress: - modules/nf-core/spring/decompress/** - tests/modules/nf-core/spring/decompress/** diff --git a/tests/modules/nf-core/spring/compress/main.nf b/tests/modules/nf-core/spring/compress/main.nf deleted file mode 100644 index 02c02a84cda..00000000000 --- a/tests/modules/nf-core/spring/compress/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SPRING_COMPRESS } from '../../../../../modules/nf-core/spring/compress/main.nf' - -workflow test_spring_compress_single_end { - - input = [ - [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - [] - ] - - SPRING_COMPRESS ( input ) -} - -workflow test_spring_compress_paired_end { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - - SPRING_COMPRESS ( input ) -} diff --git a/tests/modules/nf-core/spring/compress/nextflow.config b/tests/modules/nf-core/spring/compress/nextflow.config deleted file mode 100644 index 50f50a7a357..00000000000 --- a/tests/modules/nf-core/spring/compress/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/spring/compress/test.yml b/tests/modules/nf-core/spring/compress/test.yml deleted file mode 100644 index 42c81874ce5..00000000000 --- a/tests/modules/nf-core/spring/compress/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: spring compress test_spring_compress_single_end - command: nextflow run ./tests/modules/nf-core/spring/compress -entry test_spring_compress_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spring/compress/nextflow.config - tags: - - spring/compress - - spring - files: - - path: output/spring/test.spring - - path: output/spring/versions.yml - -- name: spring compress test_spring_compress_paired_end - command: nextflow run ./tests/modules/nf-core/spring/compress -entry test_spring_compress_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/spring/compress/nextflow.config - tags: - - spring/compress - - spring - files: - - path: output/spring/test.spring - - path: output/spring/versions.yml