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luslab-umitools | Initialized test.nf

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Candice 2020-06-01 14:39:54 +02:00
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commit bfdccfe1b9
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tools/umi_tools/dedup/test/test.nf
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#!/usr/bin/env nextflow
// Define DSL2
nextflow.preview.dsl=2
// Log
log.info ("Starting test pipeline for BAM deduplication")
/* Module inclusions
--------------------------------------------------------------------------------------*/
include umi_tools from './umi-tools.nf'
/*------------------------------------------------------------------------------------*/
/* Define input channels
--------------------------------------------------------------------------------------*/
testMetaDataBam = [
['Sample1', "$baseDir/input/prpf8_ctrl_rep1.Aligned.sortedByCoord.out.bam"],
['Sample2', "$baseDir/input/prpf8_ctrl_rep2.Aligned.sortedByCoord.out.bam"],
['Sample3', "$baseDir/input/prpf8_ctrl_rep4.Aligned.sortedByCoord.out.bam"],
['Sample4', "$baseDir/input/prpf8_eif4a3_rep1.Aligned.sortedByCoord.out.bam"],
['Sample5', "$baseDir/input/prpf8_eif4a3_rep2.Aligned.sortedByCoord.out.bam"],
['Sample6', "$baseDir/input/prpf8_eif4a3_rep4.Aligned.sortedByCoord.out.bam"]
]
testMetaDataBai = [
['Sample1', "$baseDir/input/prpf8_ctrl_rep1.Aligned.sortedByCoord.out.bai"],
['Sample2', "$baseDir/input/prpf8_ctrl_rep2.Aligned.sortedByCoord.out.bai"],
['Sample3', "$baseDir/input/prpf8_ctrl_rep4.Aligned.sortedByCoord.out.bai"],
['Sample4', "$baseDir/input/prpf8_eif4a3_rep1.Aligned.sortedByCoord.out.bai"],
['Sample5', "$baseDir/input/prpf8_eif4a3_rep2.Aligned.sortedByCoord.out.bai"],
['Sample6', "$baseDir/input/prpf8_eif4a3_rep4.Aligned.sortedByCoord.out.bai"]
]
// Create channels of test data
//Bam input channel
Channel
.from(testMetaDataBam)
.map { row -> [ row[0], file(row[1], checkIfExists: true) ]}
.set {ch_test_meta_bam}
//BamBai input channel
Channel
.from(testMetaDataBai)
.map { row -> [ row[0], file(row[1], checkIfExists: true) ] }
.join(ch_test_meta_bam)
.set {ch_test_meta_bambai}
// Run workflow
workflow {
// Run dedup
umi_tools( ch_test_meta_bambai )
// Collect file names and view output
umi_tools.out.dedupBam | view
}