mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
38ffbfdb63
* bcf annotate ready2go * edited output name * fixed output * updated bcftools ver * changed contain output string * removed contain key entirely * fixed md5sum for test.yml * using match instead of find * bcftools/annotate refactored with complete test * rm trailing white space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
process BCFTOOLS_ANNOTATE {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
|
|
'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input)
|
|
|
|
output:
|
|
tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
|
|
tuple val(meta), path("*_annotated.bcf") , optional:true , emit: bcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
|
|
def matcher = input ==~ /\S+\.*vcf\.\S*/
|
|
def output_suffix = matcher ? "vcf.gz" : "bcf"
|
|
def output_type_compressed = matcher ? "z" : "b"
|
|
"""
|
|
bcftools \\
|
|
annotate \\
|
|
$args \\
|
|
--output ${prefix}_annotated.${output_suffix} \\
|
|
--output-type $output_type_compressed \\
|
|
--threads $task.cpus \\
|
|
$input
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|