mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
process DELLY_CALL {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::delly=1.1.5" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/delly:1.1.5--h358d541_0' :
|
|
'quay.io/biocontainers/delly:1.1.5--h358d541_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input), path(input_index), path(exclude_bed)
|
|
path fasta
|
|
path fai
|
|
|
|
output:
|
|
tuple val(meta), path("*.bcf"), emit: bcf
|
|
tuple val(meta), path("*.csi"), emit: csi
|
|
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 exclude = exclude_bed ? "--exclude ${exclude_bed}" : ""
|
|
"""
|
|
delly \\
|
|
call \\
|
|
${args} \\
|
|
--outfile ${prefix}.bcf \\
|
|
--genome ${fasta} \\
|
|
${exclude} \\
|
|
${input}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
delly: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|