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Update genomescope2 module and add nf-tests (#5399)
* Add genomescope nf-test * Add stub and fitted histogram lookup table Co-authored-by: rodtheo <[email protected]> * Add snapshot * Update build version * Fix output channel contents * Update channel tests * Update tests * Lint licence Co-authored-by: rodtheo <[email protected]> * Fix linting and output file * Fix snapshot for missing file --------- Co-authored-by: rodtheo <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| nextflow_process { | ||
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| name "Test Process GENOMESCOPE2" | ||
| script "../main.nf" | ||
| config "./nextflow.config" | ||
| process "GENOMESCOPE2" | ||
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "genomescope2" | ||
| tag "meryl/count" | ||
| tag "meryl/histogram" | ||
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| setup { | ||
| run('MERYL_COUNT'){ | ||
| script "../../../../modules/nf-core/meryl/count/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.value([ | ||
| [ id: 'test', single_end: true ], // meta map | ||
| file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true ) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| run('MERYL_HISTOGRAM'){ | ||
| script "../../../../modules/nf-core/meryl/histogram/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = MERYL_COUNT.out.meryl_db | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| test("bacteroides_fragilis - fastq") { | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = MERYL_HISTOGRAM.out.hist | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert file(process.out.linear_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda | ||
| { assert file(process.out.transformed_linear_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda | ||
| { assert file(process.out.log_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda | ||
| { assert file(process.out.transformed_log_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda | ||
| { assert snapshot(process.out.model).match("model") }, | ||
| { assert snapshot(process.out.summary).match("summary") }, | ||
| { assert snapshot(process.out.lookup_table).match("lookup_table") }, | ||
| { assert file(process.out.fitted_histogram_png[0][1]).exists() }, // PNG md5sum mismatches using conda | ||
| { assert snapshot(process.out.versions).match("versions") } | ||
| ) | ||
| } | ||
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| } | ||
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| test("bacteroides_fragilis - fastq - stub") { | ||
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| options "-stub" | ||
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| when { | ||
| process { | ||
| """ | ||
| input[0] = MERYL_HISTOGRAM.out.hist | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
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| } | ||
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| } |
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