nf-core_modules/deprecated/umi_tools/test/main.nf

62 lines
2.1 KiB
Text
Raw Normal View History

#!/usr/bin/env nextflow
// Define DSL2
nextflow.preview.dsl=2
// Log
log.info ("Starting tests for umi_tools dedup...")
/*------------------------------------------------------------------------------------*/
/* Define params
--------------------------------------------------------------------------------------*/
params.umitools_dedup_args = '--umi-separator=":"'
params.verbose = false
/*------------------------------------------------------------------------------------*/
/* Module inclusions
--------------------------------------------------------------------------------------*/
include umitools_dedup from '../main.nf'
/*------------------------------------------------------------------------------------*/
/* Define input channels
--------------------------------------------------------------------------------------*/
// Define test data
testData = [
['sample1', "$baseDir/input/sample1.bam", "$baseDir/input/sample1.bai"],
['sample2', "$baseDir/input/sample2.bam", "$baseDir/input/sample2.bai"],
['sample3', "$baseDir/input/sample3.bam", "$baseDir/input/sample3.bai"],
['sample4', "$baseDir/input/sample4.bam", "$baseDir/input/sample4.bai"],
['sample5', "$baseDir/input/sample5.bam", "$baseDir/input/sample5.bai"],
['sample6', "$baseDir/input/sample6.bam", "$baseDir/input/sample6.bai"]
]
//Define test data input channel
Channel
.from(testData)
.map { row -> [ row[0], [file(row[1], checkIfExists: true), file(row[2], checkIfExists: true)]]}
.set {ch_bam}
/*------------------------------------------------------------------------------------*/
/* Run tests
--------------------------------------------------------------------------------------*/
workflow {
// Run dedup
umitools_dedup ( ch_bam )
}
workflow.onComplete {
def proc = "$baseDir/verify-checksum.sh $baseDir/../../../results/umitools/dedup/*.bam $baseDir/output/*.bam".execute()
def b = new StringBuffer()
proc.consumeProcessErrorStream(b)
log.info proc.text
errorString = b.toString()
if(errorString != '')
log.error errorString
exit 1
}