mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
|
|
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
|
|
include { PICARD_MARKDUPLICATES } from '../../../software/picard/markduplicates/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_picard_mergesamfiles {
|
|
|
|
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.name.sorted.bam", checkIfExists: true), ] ]
|
|
|
|
PICARD_MERGESAMFILES ( input )
|
|
}
|
|
|
|
|
|
workflow test_picard_collectmultiplemetrics {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
|
|
|
PICARD_COLLECTMULTIPLEMETRICS (
|
|
input,
|
|
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
|
)
|
|
}
|
|
|
|
workflow test_picard_markduplicates {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
|
|
PICARD_MARKDUPLICATES ( input )
|
|
}
|
|
|
|
workflow test_picard_markduplicates_not_sorted {
|
|
|
|
def input = []
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
|
|
|
PICARD_MARKDUPLICATES ( input )
|
|
}
|