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21 lines
841 B
Text
21 lines
841 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CNVKIT } from '../../../software/cnvkit/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
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workflow test_cnvkit {
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tumourbam = [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_paired_end.sorted.bam", checkIfExists: true) ]
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normalbam = [ file("${launchDir}/tests/data/genomics/sarscov2/bam/test_single_end.sorted.bam", checkIfExists: true) ]
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def input = []
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input = [ [ id:'test' ], // meta map
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tumourbam, normalbam ]
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fasta = [ file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) ]
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targetfile = [ file("${launchDir}/tests/data/genomics/sarscov2/bed/baits.bed", checkIfExists: true) ]
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CNVKIT ( input, fasta, targetfile )
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}
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