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Merge pull request #129 from nf-core/fix/ci-nf-tests
Fix/ci nf tests & Remove un-necessary registry declarations
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,17 @@ | ||
| config { | ||
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| // location for all nf-tests | ||
| testsDir "tests" | ||
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| // nf-test directory including temporary files for each test | ||
| workDir ".nf-test" | ||
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| // location of library folder that is added automatically to the classpath | ||
| libDir "tests/pipeline/lib/" | ||
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| // location of an optional nextflow.config file specific for executing tests | ||
| configFile "nextflow.config" | ||
| profile "test" | ||
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| // run all test with the defined docker profile from the main nextflow.config | ||
| profile "" | ||
| } | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| nextflow_pipeline { | ||
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| name "Test Workflow main.nf" | ||
| script "main.nf" | ||
| tag "bases2fastq" | ||
| tag "pipeline" | ||
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| test("Bases2Fastq") { | ||
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| when { | ||
| params { | ||
| input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/b2fq-samplesheet.csv' | ||
| demultiplexer = 'bases2fastq' | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, | ||
| { assert workflow.trace.succeeded().size() == 8 }, | ||
| { assert snapshot( | ||
| // FIXME | ||
| // path("$outputDir/sim-data/DefaultSample_R1.fastq.gz.md5"), | ||
| // path("$outputDir/sim-data/DefaultSample_R2.fastq.gz.md5"), | ||
| path("$outputDir/sim-data/Metrics.csv"), | ||
| path("$outputDir/sim-data/RunManifest.json"), | ||
| path("$outputDir/sim-data/UnassignedSequences.csv"), | ||
| path("$outputDir/sim-data/Samples/DefaultSample/DefaultSample_R1.fastq.gz"), | ||
| path("$outputDir/sim-data/Samples/DefaultSample/DefaultSample_R2.fastq.gz"), | ||
| ).match("bases2fastq") }, | ||
| { assert new File("$outputDir/sim-data/Bases2Fastq-Sim_QC.html").exists() }, | ||
| { assert new File("$outputDir/sim-data/RunStats.json").exists() }, | ||
| { assert new File("$outputDir/sim-data/Samples/DefaultSample/DefaultSample_stats.json").exists() } | ||
| ) | ||
| } | ||
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| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| { | ||
| "software_versions": { | ||
| "content": [ | ||
| "{BASES2FASTQ={bases2fastq=1.1.0.593880262, use subject to license available at elementbiosciences.com}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" | ||
| ], | ||
| "timestamp": "2023-06-15T00:10:15+0000" | ||
| }, | ||
| "bases2fastq": { | ||
| "content": [ | ||
| "Metrics.csv:md5,3213ad7bdf66f33476cb589b4d608948", | ||
| "RunManifest.json:md5,d4ecdb19e5fbcffab3e6e770c34023fb", | ||
| "UnassignedSequences.csv:md5,11c1693830ce941b8cfb8d2431a59097", | ||
| "DefaultSample_R1.fastq.gz:md5,77b68ec94323741d1bddc03a7a428fa9", | ||
| "DefaultSample_R2.fastq.gz:md5,ecd4ed53e10207582bbbc29383080b57" | ||
| ], | ||
| "timestamp": "2023-06-15T00:10:15+0000" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| nextflow_pipeline { | ||
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| name "Test Workflow main.nf" | ||
| script "main.nf" | ||
| tag "bcl2fastq" | ||
| tag "pipeline" | ||
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| test("Bcl2Fastq") { | ||
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| when { | ||
| params { | ||
| input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' | ||
| demultiplexer = 'bcl2fastq' | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, | ||
| { assert workflow.trace.succeeded().size() == 6 }, | ||
| { assert snapshot( | ||
| // FIXME | ||
| // path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz.md5"), | ||
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| path("$outputDir/bcl2fastq/Sample1_S1_L001_R1_001.fastq.gz"), | ||
| path("$outputDir/bcl2fastq/Stats").list(), | ||
| ).match("bcl2fastq") } | ||
| ) | ||
| } | ||
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| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| nextflow_pipeline { | ||
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| name "Test Workflow main.nf" | ||
| script "main.nf" | ||
| tag "bclconvert" | ||
| tag "pipeline" | ||
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| test("BCL-CONVERT") { | ||
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| when { | ||
| params { | ||
| input = 'https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/samplesheet/1.3.0/flowcell_input.csv' | ||
| demultiplexer = 'bclconvert' | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, | ||
| { assert workflow.trace.succeeded().size() == 6 }, | ||
| { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bylane.txt"), | ||
| path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), | ||
| path("$outputDir/multiqc/multiqc_data/multiqc_bclconvert_bysample.txt")).match("multiqc") }, | ||
| { assert snapshot(path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001.fastp.fastq.gz"), | ||
| path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_R1_001.fastq.gz"), | ||
| path("$outputDir/220422_M11111_0222_000000000-K9H97/Sample1_S1_L001_summary.txt"), | ||
| path("$outputDir/220422_M11111_0222_000000000-K9H97/Undetermined_S0_L001_R1_001.fastq.gz"), | ||
| path("$outputDir/220422_M11111_0222_000000000-K9H97/L001/Reports/").list(), | ||
| ).match("bclconvert") } | ||
| ) | ||
| } | ||
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| } | ||
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| } |
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