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47 lines
1.4 KiB
Text
47 lines
1.4 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { VCFTOOLS as VCFTOOLS_BASE} from '../../../software/vcftools/main.nf' addParams( options: ['args': '--freq'] )
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include { VCFTOOLS as VCFTOOLS_OPTIONAL} from '../../../software/vcftools/main.nf' addParams( options: ['args': '--freq --exclude-bed'] )
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workflow test_vcftools_vcf_base {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]
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VCFTOOLS_BASE ( input, [], [] )
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}
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workflow test_vcftools_vcfgz_base {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ]
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VCFTOOLS_BASE ( input, [], [] )
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}
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workflow test_vcftools_vcf_optional {
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def input = []
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def bed = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true) ]
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VCFTOOLS_OPTIONAL ( input, bed, [] )
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}
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workflow test_vcftools_vcfgz_optional {
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def input = []
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def bed = file("${launchDir}/tests/data/genomics/sarscov2/bed/test.bed", checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf.gz", checkIfExists: true) ]
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VCFTOOLS_OPTIONAL ( input, bed, [] )
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}
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