nf-core_modules/tests/software/bcftools/consensus/main.nf
Mark-S-Hill 889465cb2b
update test data paths (#373)
* update test data paths

* Update test md5sums

* gatk test fixes & update variantfiltration main

* few extra fixes after review

* fix suspected format error

* Update software/gatk4/variantfiltration/main.nf

* Update software/gatk4/variantfiltration/main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
workflow test_bcftools_consensus {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
]
BCFTOOLS_CONSENSUS ( input )
}