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https://github.com/MillironX/nf-core_modules.git
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86 lines
3 KiB
Text
86 lines
3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BEDTOOLS_COMPLEMENT } from '../../../software/bedtools/complement/main.nf' addParams( options: [:] )
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include { BEDTOOLS_GENOMECOV } from '../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
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include { BEDTOOLS_INTERSECT } from '../../../software/bedtools/intersect/main.nf' addParams( options: [:] )
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include { BEDTOOLS_MERGE } from '../../../software/bedtools/merge/main.nf' addParams( options: [:] )
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include { BEDTOOLS_SLOP as BEDTOOLS_SLOP_S} from '../../../software/bedtools/slop/main.nf' addParams( options: [:] )
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include { BEDTOOLS_SLOP as BEDTOOLS_SLOP_AS} from '../../../software/bedtools/slop/main.nf' addParams( options: [:] )
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include { BEDTOOLS_SORT } from '../../../software/bedtools/sort/main.nf' addParams( options: [publish_dir: 'test_bedtools_sort'] ) // needed for merge
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workflow test_bedtools_complement {
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
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file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
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BEDTOOLS_COMPLEMENT( input )
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}
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workflow test_bedtools_genomecov {
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
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file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
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BEDTOOLS_GENOMECOV( input )
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}
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workflow test_bedtools_intersect {
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
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file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ] //metamap
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BEDTOOLS_INTERSECT( input )
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}
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// TODO use output of sort module
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workflow test_bedtools_merge {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
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BEDTOOLS_MERGE(input)
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}
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// TODO streamline slop module
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// To run with header and pct enabled, type --pct true and --header true with nextflow run command.
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/*
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Test with l/r method
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*/
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workflow test_bedtools_slop_asymmetrical {
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def input = []
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input = [ [ id:'test', symmetry: false],
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file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
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file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
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BEDTOOLS_SLOP_AS( input )
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}
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/*
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Test with b method
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*/
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workflow test_bedtools_slop_symmetrical {
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def input = []
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input = [ [ id:'test', symmetry: true],
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file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
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file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
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BEDTOOLS_SLOP_S( input )
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}
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workflow test_bedtools_sort {
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def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
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BEDTOOLS_SORT( input )
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emit:
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sort = BEDTOOLS_SORT.out.sort
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}
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