nf-core_modules/tests/software/vcftools/main.nf

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