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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,19 @@ | ||
| config { | ||
| // location for all nf-tests | ||
| testsDir "tests/pipeline" | ||
| testsDir "." | ||
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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/lib/" | ||
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| // location of an optional nextflow.config file specific for executing tests | ||
| configFile "nextflow.config" | ||
| configFile "conf/test.config" | ||
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| // run all test with defined profile(s) from the main nextflow.config | ||
| profile "" | ||
| profile "test" | ||
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| // Include plugins | ||
| plugins { | ||
| load "[email protected]" | ||
| load "[email protected]" | ||
| } | ||
| } |
12 changes: 6 additions & 6 deletions
12
subworkflows/local/gens_pon.nf → subworkflows/local/gens_pon/main.nf
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28 changes: 14 additions & 14 deletions
28
...rkflows/local/germlinecnvcaller_cohort.nf → ...ws/local/germlinecnvcaller_cohort/main.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| multiqc/multiqc_data/multiqc.log | ||
| multiqc/multiqc_data/multiqc_data.json | ||
| multiqc/multiqc_data/multiqc_general_stats.txt | ||
| multiqc/multiqc_data/multiqc_software_versions.txt | ||
| multiqc/multiqc_data/multiqc_sources.txt | ||
| multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} | ||
| multiqc/multiqc_report.html | ||
| pipeline_info/*.{html,json,txt,yml} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| nextflow_pipeline { | ||
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| name "Test pipeline" | ||
| script "../main.nf" | ||
| tag "pipeline" | ||
| tag "pipeline_createpanelrefs" | ||
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| test("Run with profile test | default aka cnvkit") { | ||
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| when { | ||
| params { | ||
| 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_ceatepanelrefs_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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| nextflow_pipeline { | ||
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| name "Test pipeline | gens" | ||
| script "../main.nf" | ||
| tag "pipeline" | ||
| tag "pipeline_createpanelrefs" | ||
| config "./gens_pon.config" | ||
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| test("Run gens test") { | ||
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| when { | ||
| params { | ||
| fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" | ||
| gens_bin_length = 100 | ||
| gens_pon_name = 'gens_pon' | ||
| gens_readcount_format = "TSV" | ||
| outdir = "$outputDir" | ||
| tools = 'gens' | ||
| } | ||
| } | ||
|
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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_ceatepanelrefs_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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| nextflow_pipeline { | ||
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| name "Test pipeline | germlinecnvcaller" | ||
| script "../main.nf" | ||
| tag "pipeline" | ||
| tag "pipeline_createpanelrefs" | ||
| config "./germlinecnvcaller_cohort.config" | ||
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| test("Run germlinecnvcaller test") { | ||
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| when { | ||
| params { | ||
| fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" | ||
| gcnv_model_name = 'cohort' | ||
| gcnv_ploidy_priors = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" | ||
| gcnv_scatter_content = 2 | ||
| outdir = "$outputDir" | ||
| tools = 'germlinecnvcaller' | ||
| } | ||
| } | ||
|
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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_ceatepanelrefs_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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| nextflow_pipeline { | ||
|
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| name "Test MUTECT2_PON" | ||
| script "main.nf" | ||
| tag "MUTECT2" | ||
|
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| test("Run MUTECT2 test") { | ||
|
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| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| tools = 'mutect2' | ||
| mutect2_pon_name = 'test' | ||
| } | ||
| } | ||
|
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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_ceatepanelrefs_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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