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Merge pull request #1467 from nf-core/test_umi
Add test suite for UMI handling functionality
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| nextflow_pipeline { | ||
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| name "Test pipeline with dummy UMI settings" | ||
| script "../main.nf" | ||
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| test("Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'") { | ||
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| when { | ||
| params { | ||
| with_umi = true | ||
| umitools_extract_method = "regex" | ||
| umitools_bc_pattern = "^(?P<umi_1>CGA.{8}){s<=2}.*" | ||
| umitools_dedup_stats = true | ||
| skip_bbsplit = true | ||
| umi_dedup_tool = 'umicollapse' | ||
| aligner = 'hisat2' | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
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| then { | ||
| // stable_name: All files + folders in ${params.outdir}/ with a stable name | ||
| def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) | ||
| // stable_path: All files in ${params.outdir}/ with stable content | ||
| def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot( | ||
| // Number of successful tasks | ||
| workflow.trace.succeeded().size(), | ||
| // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions | ||
| removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), | ||
| // All stable path name, with a relative path | ||
| stable_name, | ||
| // All files with stable contents | ||
| stable_path | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
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| test("--umi_dedup_tool 'umitools'") { | ||
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| when { | ||
| params { | ||
| with_umi = true | ||
| umitools_extract_method = "regex" | ||
| umitools_bc_pattern = "^(?P<umi_1>CGA.{8}){s<=2}.*" | ||
| umitools_dedup_stats = true | ||
| skip_bbsplit = true | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
|
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||
| then { | ||
| // stable_name: All files + folders in ${params.outdir}/ with a stable name | ||
| def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) | ||
| // stable_path: All files in ${params.outdir}/ with stable content | ||
| def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot( | ||
| // Number of successful tasks | ||
| workflow.trace.succeeded().size(), | ||
| // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions | ||
| removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), | ||
| // All stable path name, with a relative path | ||
| stable_name, | ||
| // All files with stable contents | ||
| stable_path | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
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| test("--umi_dedup_tool 'umitools - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| params { | ||
| with_umi = true | ||
| umitools_extract_method = "regex" | ||
| umitools_bc_pattern = "^(?P<umi_1>CGA.{8}){s<=2}.*" | ||
| umitools_dedup_stats = true | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| // stable_name: All files + folders in ${params.outdir}/ with a stable name | ||
| def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) | ||
| // stable_path: All files in ${params.outdir}/ with stable content | ||
| def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot( | ||
| // Number of successful tasks | ||
| workflow.trace.succeeded().size(), | ||
| // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions | ||
| removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), | ||
| // All stable path name, with a relative path | ||
| stable_name, | ||
| // All files with stable contents | ||
| stable_path | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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