diff --git a/modules/nf-core/bcl2fastq/tests/main.nf.test b/modules/nf-core/bcl2fastq/tests/main.nf.test new file mode 100644 index 00000000000..ca03b972893 --- /dev/null +++ b/modules/nf-core/bcl2fastq/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test Process BCL2FASTQ" + script "modules/nf-core/bcl2fastq/main.nf" + process "BCL2FASTQ" + config "./nextflow.config" + tag "bcl2fastq" + tag "modules" + tag "modules_nfcore" + + test("homo sapiens illumina [bcl]") { + when { + process { + //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996 + """ + input[0] = [ + [ id: 'test', lane:1 ], + file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git 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00000000000..991d1761711 --- /dev/null +++ b/modules/nf-core/bcl2fastq/tests/tags.yml @@ -0,0 +1,2 @@ +bcl2fastq: + - modules/nf-core/bcl2fastq/** diff --git a/modules/nf-core/bclconvert/tests/main.nf.test b/modules/nf-core/bclconvert/tests/main.nf.test new file mode 100644 index 00000000000..ec0623afa8e --- /dev/null +++ b/modules/nf-core/bclconvert/tests/main.nf.test @@ -0,0 +1,41 @@ +nextflow_process { + + name "Test Process BCLCONVERT" + script "../main.nf" + process "BCLCONVERT" + config "./nextflow.config" + tag "bclconvert" + tag "modules" + tag "modules_nfcore" + + test("homo sapiens illumina [bcl]") { + when { + process { + //TODO use new test dataset when available, see https://github.com/nf-core/test-datasets/issues/996 + """ + input[0] = [ + [ id: 'test', lane:1 ], + file(params.test_data['homo_sapiens']['illumina']['test_flowcell_samplesheet'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.reports, + process.out.versions, + process.out.fastq, + process.out.undetermined, + file(process.out.logs.get(0).get(1)).list().sort(), + process.out.interop.get(0).get(1).findAll { file(it).name != "IndexMetricsOut.bin" }, + ).match() + }, + { assert file(process.out.interop.get(0).get(1).find { file(it).name == "IndexMetricsOut.bin" }).exists() } + ) + } + } +} diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap new file mode 100644 index 00000000000..8f67e89968c --- /dev/null +++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "homo sapiens illumina [bcl]": { + "content": [ + [ + [ + { + "id": "test", + "lane": 1 + }, + [ + "Adapter_Cycle_Metrics.csv:md5,5a0c88793b4a0885fe3dda16609b576e", + "Adapter_Metrics.csv:md5,989240b8840b2169ac1061f952c90f6c", + 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"FastqComplete.txt", + "Info.log", + "Warnings.log" + ], + [ + "ControlMetricsOut.bin:md5,6d77b38d0793a6e1ce1e85706e488953", + "CorrectedIntMetricsOut.bin:md5,2bbf84d3be72734addaa2fe794711434", + "ErrorMetricsOut.bin:md5,38c88def138e9bb832539911affdb286", + "ExtractionMetricsOut.bin:md5,7497c3178837eea8f09350b5cd252e99", + "QMetricsOut.bin:md5,7e9f198d53ebdfbb699a5f94cf1ed51c", + "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c" + ] + ], + "timestamp": "2023-10-25T12:22:57.986028" + } +} \ No newline at end of file diff --git a/modules/nf-core/bclconvert/tests/nextflow.config b/modules/nf-core/bclconvert/tests/nextflow.config new file mode 100644 index 00000000000..344f4720cf9 --- /dev/null +++ b/modules/nf-core/bclconvert/tests/nextflow.config @@ -0,0 +1,10 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + ext.args = {[ + meta.lane ? "--bcl-only-lane ${meta.lane}" : "", + "--force", + "--first-tile-only true" + ].join(" ").trim()} +} diff --git a/modules/nf-core/bclconvert/tests/tags.yml b/modules/nf-core/bclconvert/tests/tags.yml new file mode 100644 index 00000000000..da3e03d57f8 --- /dev/null +++ b/modules/nf-core/bclconvert/tests/tags.yml @@ -0,0 +1,2 @@ +bclconvert: + - modules/nf-core/bclconvert/** diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index b6d733dc1e7..db925b6837d 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -331,16 +331,6 @@ bcftools/view: - modules/nf-core/bcftools/view/** - tests/modules/nf-core/bcftools/view/** -bcl2fastq: - - modules/nf-core/bcl2fastq/** - - modules/nf-core/untar/** - - tests/modules/nf-core/bcl2fastq/** - -bclconvert: - - modules/nf-core/bclconvert/** - - modules/nf-core/untar/** - - tests/modules/nf-core/bclconvert/** - beagle5/beagle: - modules/nf-core/beagle5/beagle/** - tests/modules/nf-core/beagle5/beagle/**