mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
40 lines
1.1 KiB
Text
40 lines
1.1 KiB
Text
process ALLELECOUNTER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0' :
|
|
'quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input), path(input_index)
|
|
path loci
|
|
path fasta
|
|
|
|
output:
|
|
tuple val(meta), path("*.alleleCount"), emit: allelecount
|
|
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 reference_options = fasta ? "-r $fasta": ""
|
|
|
|
"""
|
|
alleleCounter \\
|
|
$args \\
|
|
-l $loci \\
|
|
-b $input \\
|
|
$reference_options \\
|
|
-o ${prefix}.alleleCount
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
allelecounter: \$(alleleCounter --version)
|
|
END_VERSIONS
|
|
"""
|
|
}
|