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https://github.com/MillironX/nf-core_modules.git
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65 lines
2.1 KiB
Text
65 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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//keep arg of bcftools_filter, otherwise md5 will change on each execution
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include { BCFTOOLS_FILTER } from '../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
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include { BCFTOOLS_STATS } from '../../../software/bcftools/stats/main.nf' addParams( options: [:] )
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include { BCFTOOLS_BGZIP } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
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include { BCFTOOLS_TABIX } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
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include { BCFTOOLS_CONSENSUS } from '../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
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workflow test_bcftools_filter {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_FILTER ( input )
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}
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workflow test_bcftools_stats {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_STATS ( input )
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}
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workflow test_bcftools_bgzip {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_BGZIP ( input )
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}
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workflow test_bcftools_tabix {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_BGZIP ( input )
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BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
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}
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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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