mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
64 lines
2.1 KiB
Text
64 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BEDTOOLS_COMPLEMENT } from '../../../software/bedtools/complement/main.nf' addParams( options: [:] )
|
|
include { BEDTOOLS_GENOMECOV } from '../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
|
|
include { BEDTOOLS_INTERSECT } from '../../../software/bedtools/intersect/main.nf' addParams( options: [:] )
|
|
include { BEDTOOLS_MERGE } from '../../../software/bedtools/merge/main.nf' addParams( options: [:] )
|
|
include { BEDTOOLS_SLOP} from '../../../software/bedtools/slop/main.nf' addParams( options: [args: '-l 15 -r 30'] )
|
|
include { BEDTOOLS_SORT } from '../../../software/bedtools/sort/main.nf' addParams( options: [:] )
|
|
|
|
|
|
workflow test_bedtools_complement {
|
|
def input = []
|
|
input = [ [ id:'test'],
|
|
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
|
|
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
|
|
|
|
BEDTOOLS_COMPLEMENT( input )
|
|
}
|
|
|
|
workflow test_bedtools_genomecov {
|
|
def input = []
|
|
input = [ [ id:'test'],
|
|
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
|
|
|
|
BEDTOOLS_GENOMECOV( input )
|
|
}
|
|
|
|
workflow test_bedtools_intersect {
|
|
def input = []
|
|
input = [ [ id:'test'],
|
|
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
|
|
file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ] //metamap
|
|
|
|
BEDTOOLS_INTERSECT( input )
|
|
}
|
|
|
|
|
|
workflow test_bedtools_merge {
|
|
def input = []
|
|
input = [ [ id:'test' ], // meta map
|
|
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
|
|
BEDTOOLS_MERGE(input)
|
|
}
|
|
|
|
workflow test_bedtools_slop {
|
|
def input = []
|
|
input = [ [ id:'test'],
|
|
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
|
|
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
|
|
BEDTOOLS_SLOP ( input )
|
|
}
|
|
|
|
workflow test_bedtools_sort {
|
|
def input = []
|
|
input = [ [ id:'test'],
|
|
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
|
|
|
|
BEDTOOLS_SORT( input )
|
|
|
|
}
|
|
|
|
|