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24 lines
1 KiB
Text
24 lines
1 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
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include { BCFTOOLS_TABIX as BCFTOOLS_TABIX } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
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include { BCFTOOLS_CONSENSUS as BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
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workflow test_bcftools_consensus {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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def fasta = []
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fasta = Channel.of ([ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ])
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BCFTOOLS_BGZIP ( input )
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BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
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BCFTOOLS_CONSENSUS ( BCFTOOLS_BGZIP.out.vcf
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.join( BCFTOOLS_TABIX.out.tbi, by: [0] )
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.join( fasta, by: [0] ) )
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}
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