mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
58 lines
2.1 KiB
Text
58 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
|
|
include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
|
|
include { SAMTOOLS_INDEX } from '../../../software/samtools/index/main.nf' addParams( options: [:] )
|
|
include { SAMTOOLS_SORT } from '../../../software/samtools/sort/main.nf' addParams( options: [:] )
|
|
include { SAMTOOLS_STATS } from '../../../software/samtools/stats/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_samtools_flagstat {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
|
|
SAMTOOLS_FLAGSTAT ( input )
|
|
}
|
|
|
|
workflow test_samtools_idxstats {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
|
|
SAMTOOLS_IDXSTATS ( input )
|
|
}
|
|
|
|
workflow test_samtools_index {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
|
|
SAMTOOLS_INDEX ( input )
|
|
}
|
|
|
|
// FIXME Why is this passing it an already sorted bam?
|
|
workflow test_samtools_sort {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
|
|
SAMTOOLS_SORT ( input )
|
|
}
|
|
|
|
workflow test_samtools_stats {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
|
|
|
|
SAMTOOLS_STATS ( input )
|
|
}
|