mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
62 lines
No EOL
2.1 KiB
Text
62 lines
No EOL
2.1 KiB
Text
#!/usr/bin/env nextflow
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// Define DSL2
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nextflow.preview.dsl=2
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// Log
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log.info ("Starting tests for umi_tools dedup...")
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/*------------------------------------------------------------------------------------*/
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/* Define params
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--------------------------------------------------------------------------------------*/
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params.umitools_dedup_args = '--umi-separator=":"'
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params.verbose = false
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/*------------------------------------------------------------------------------------*/
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/* Module inclusions
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--------------------------------------------------------------------------------------*/
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include umitools_dedup from '../main.nf'
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/*------------------------------------------------------------------------------------*/
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/* Define input channels
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--------------------------------------------------------------------------------------*/
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// Define test data
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testData = [
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['sample1', "$baseDir/input/sample1.bam", "$baseDir/input/sample1.bai"],
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['sample2', "$baseDir/input/sample2.bam", "$baseDir/input/sample2.bai"],
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['sample3', "$baseDir/input/sample3.bam", "$baseDir/input/sample3.bai"],
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['sample4', "$baseDir/input/sample4.bam", "$baseDir/input/sample4.bai"],
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['sample5', "$baseDir/input/sample5.bam", "$baseDir/input/sample5.bai"],
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['sample6', "$baseDir/input/sample6.bam", "$baseDir/input/sample6.bai"]
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]
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//Define test data input channel
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Channel
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.from(testData)
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.map { row -> [ row[0], [file(row[1], checkIfExists: true), file(row[2], checkIfExists: true)]]}
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.set {ch_bam}
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/*------------------------------------------------------------------------------------*/
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/* Run tests
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--------------------------------------------------------------------------------------*/
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workflow {
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// Run dedup
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umitools_dedup ( ch_bam )
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}
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workflow.onComplete {
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def proc = "$baseDir/verify-checksum.sh $baseDir/../../../results/umitools/dedup/*.bam $baseDir/output/*.bam".execute()
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def b = new StringBuffer()
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proc.consumeProcessErrorStream(b)
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log.info proc.text
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errorString = b.toString()
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if(errorString != '')
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log.error errorString
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exit 1
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} |