nf-core_modules/modules/bcftools/annotate/main.nf
Mei Wu 38ffbfdb63
bcftools/annotate follow up corrections (#1359)
* 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>
2022-02-28 10:16:29 -05:00

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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
"""
}