nf-core_modules/modules/allelecounter/main.nf
2022-02-04 09:53:32 +01:00

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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
"""
}