mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
62 lines
No EOL
2.1 KiB
Text
62 lines
No EOL
2.1 KiB
Text
#!/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
|
|
} |