mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
68 lines
No EOL
2.1 KiB
Text
68 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 test 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 = true
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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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// Meta data
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testMetaDataBam = [
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['sample1', "$baseDir/input/sample1.bam"],
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['sample2', "$baseDir/input/sample2.bam"],
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['sample3', "$baseDir/input/sample3.bam"],
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['sample4', "$baseDir/input/sample4.bam"],
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['sample5', "$baseDir/input/sample5.bam"],
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['sample6', "$baseDir/input/sample6.bam"]
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]
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testMetaDataBai = [
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['sample1', "$baseDir/input/sample1.bai"],
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['sample2', "$baseDir/input/sample2.bai"],
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['sample3', "$baseDir/input/sample3.bai"],
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['sample4', "$baseDir/input/sample4.bai"],
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['sample5', "$baseDir/input/sample5.bai"],
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['sample6', "$baseDir/input/sample6.bai"]
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]
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//Bam input channel
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Channel
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.from(testMetaDataBam)
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.map { row -> [ row[0], file(row[1], checkIfExists: true) ]}
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.set {ch_test_meta_bam}
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//BamBai input channel
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Channel
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.from(testMetaDataBai)
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.map { row -> [ row[0], file(row[1], checkIfExists: true) ] }
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.join(ch_test_meta_bam)
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.set {ch_test_meta_bambai}
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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_test_meta_bambai )
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// Collect file names and view output
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umitools_dedup.out.dedupBam | view
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} |