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

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2021-02-02 08:14:00 +00:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCFTOOLS_FILTER } from '../../../software/bcftools/filter/main.nf' addParams( options: [:] )
include { BCFTOOLS_STATS } from '../../../software/bcftools/stats/main.nf' addParams( options: [:] )
include { BCFTOOLS_BGZIP } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
include { BCFTOOLS_TABIX } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
include { BCFTOOLS_CONSENSUS } from '../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
workflow test_bcftools_filter {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
BCFTOOLS_FILTER ( input )
}
workflow test_bcftools_stats {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
BCFTOOLS_STATS ( input )
}
workflow test_bcftools_bgzip {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
BCFTOOLS_BGZIP ( input )
}
workflow test_bcftools_tabix {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
BCFTOOLS_BGZIP ( input )
BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
}
workflow test_bcftools_consensus {
def input = []
input = [ [ id:'test' ], // meta map
file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
def fasta = []
fasta = Channel.of ([ [ id:'test' ], // meta map
file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ])
BCFTOOLS_BGZIP ( input )
BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
BCFTOOLS_CONSENSUS ( BCFTOOLS_BGZIP.out.vcf
.join( BCFTOOLS_TABIX.out.tbi, by: [0] )
.join( fasta, by: [0] ) )
}