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https://github.com/MillironX/nf-core_modules.git
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44 lines
2 KiB
Text
44 lines
2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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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_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
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include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP2 } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
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include { BCFTOOLS_TABIX as BCFTOOLS_TABIX2 } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
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include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP3 } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
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include { BCFTOOLS_TABIX as BCFTOOLS_TABIX3 } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
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workflow test_bcftools_isec {
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def input1, input2, input3 = []
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input1 = [ [ id:'test1' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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input2 = [ [ id:'test2' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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input3 = [ [ id:'test3' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_BGZIP ( input1 )
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BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
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BCFTOOLS_BGZIP2 ( input2 )
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BCFTOOLS_TABIX2 ( BCFTOOLS_BGZIP2.out.vcf )
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BCFTOOLS_BGZIP3 ( input3 )
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BCFTOOLS_TABIX3 ( BCFTOOLS_BGZIP3.out.vcf )
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vcfs = BCFTOOLS_BGZIP.out.vcf
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.mix( BCFTOOLS_BGZIP2.out.vcf )
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.mix( BCFTOOLS_BGZIP3.out.vcf )
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.map { [ it[1] ]}.collect().map { [ [id: 'test'], it ] }
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tbis = BCFTOOLS_TABIX.out.tbi
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.mix( BCFTOOLS_TABIX2.out.tbi )
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.mix( BCFTOOLS_TABIX3.out.tbi )
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.map { [ it[1] ]}.collect().map { [ [id: 'test'], it ] }
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BCFTOOLS_ISEC ( vcfs.join(tbis) )
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}
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