nf-core_modules/modules/bcftools/consensus/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process BCFTOOLS_CONSENSUS {
tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::bcftools=1.11' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container 'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0'
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} else {
container 'quay.io/biocontainers/bcftools:1.11--h7c999a4_0'
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}
input:
tuple val(meta), path(vcf), path(tbi), path(fasta)
output:
tuple val(meta), path('*.fa'), emit: fasta
path '*.version.txt' , emit: version
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script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
cat $fasta | bcftools consensus $vcf $options.args > ${prefix}.fa
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
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echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
"""
}