mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
39 lines
1.1 KiB
Text
39 lines
1.1 KiB
Text
process LOFREQ_CALLPARALLEL {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
|
|
'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
path fasta
|
|
path fai
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
|
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}"
|
|
"""
|
|
lofreq \\
|
|
call-parallel \\
|
|
--pp-threads $task.cpus \\
|
|
$args \\
|
|
-f $fasta \\
|
|
-o ${prefix}.vcf.gz \\
|
|
$bam
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|