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luslab-umitools | Combined bam/bai into single channel + clean up
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parent
cb58bea33f
commit
3e26c218c2
2 changed files with 19 additions and 36 deletions
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@ -14,7 +14,7 @@ process umitools_dedup {
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container 'luslab/nf-modules-umitools:latest'
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input:
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tuple val(sample_id), path(bai), path(bam)
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tuple val(sample_id), path(bam)
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output:
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tuple val(sample_id), path("*.dedup.bam"), emit: dedupBam
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@ -23,25 +23,24 @@ process umitools_dedup {
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script:
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// Init
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internal_prog = "umi_tools dedup"
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args = "--log=${sample_id}.dedup.log"
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// Check main args string exists and strip whitespace
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if(params.umitools_dedup_args) {
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ext_args = params.umitools_dedup_args
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internal_args += " " + ext_args.trim()
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args += " " + ext_args.trim()
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}
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// Contruct CL line
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command = "${internal_prog} ${internal_args} -I $bam -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
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command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
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// Log
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if (params.verbose){
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println ("[MODULE] umi_tools/dedup exec: " + internal_cl)
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println ("[MODULE] umi_tools/dedup exec: " + command)
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}
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//SHELL
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"""
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${internal_cl}
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${command}
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"""
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}
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@ -4,7 +4,7 @@
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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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log.info ("Starting tests for umi_tools dedup...")
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/*------------------------------------------------------------------------------------*/
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/* Define params
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@ -23,37 +23,21 @@ include umitools_dedup from '../main.nf'
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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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// 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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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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//Define test data 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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.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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@ -61,7 +45,7 @@ Channel
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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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umitools_dedup ( ch_bam )
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// Collect file names and view output
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umitools_dedup.out.dedupBam | view
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