mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
49 lines
1.6 KiB
Text
49 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process BCFTOOLS_REHEADER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
publishDir "${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 fai
|
|
path header
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def update_sequences = fai ? "-f $fai" : ""
|
|
def new_header = header ? "-h $header" : ""
|
|
"""
|
|
bcftools \\
|
|
reheader \\
|
|
$update_sequences \\
|
|
$new_header \\
|
|
$options.args \\
|
|
--threads $task.cpus \\
|
|
-o ${prefix}.vcf.gz \\
|
|
$vcf
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|