mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
c5235a983d
* Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
38 lines
1.4 KiB
Text
38 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BCFTOOLS_CONSENSUS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
publishDir "${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']) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0'
|
|
} else {
|
|
container 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(vcf), path(tbi), path(fasta)
|
|
|
|
output:
|
|
tuple val(meta), path('*.fa'), emit: fasta
|
|
path '*.version.txt' , emit: version
|
|
|
|
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
|
|
|
|
echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
|
|
"""
|
|
}
|