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Updated module, need to fix cardinality of tuple
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2 changed files with 10 additions and 10 deletions
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@ -1,10 +1,10 @@
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// Import generic module functions
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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params.options = [upstream: 1,
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def options = initOptions(params.options)
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downstream: 10 ]
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def VERSION = '2.29'
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def options = initOptions(params.options)
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process BEDTOOLS_SLOPREFSEQ {
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process BEDTOOLS_SLOPREFSEQ {
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tag "$meta.id"
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tag "$meta.id"
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@ -33,7 +33,7 @@ process BEDTOOLS_SLOPREFSEQ {
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def beds_files = beds.sort()
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def beds_files = beds.sort()
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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"""
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slopBed -i $beds -g $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed
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slopBed -i ln -s ${beds[0]} -g ln -s $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed
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echo $VERSION > ${software}.version.txt
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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"""
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"""
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}
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}
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nextflow.preview.dsl = 2
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nextflow.preview.dsl = 2
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include BEDTOOLS_SLOPREFSEQ from '../sloprefseq/main.nf' addParams( options: [publish_dir:'test_bed_file'])
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include { BEDTOOLS_SLOPREFSEQ } from '../../sloprefseq/main.nf' addParams( options: [publish_dir:'test_bed_file'])
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// Define input channels
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// Define input channels
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// Run the workflow
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// Run the workflow
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workflow test_bed_file{
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workflow test_bed_file{
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def input = []
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def input = []
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input = [ [ id:'test' ],
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input = [ [ id:'test', single_end:true ],
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[ file("${baseDir}/input/A.bed", checkIfExists: true),
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[ file("${baseDir}/input/A.bed", checkIfExists: true),
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file("${baseDir}/input/genome.sizes", checkIfExists: true)] ]
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file("${baseDir}/input/genome.sizes", checkIfExists: true) ] ]
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BEDTOOLS_SLOPREFSEQ ( input )
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BEDTOOLS_SLOPREFSEQ ( input, [ publish_dir:'test_bed_file' ] )
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}
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}
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