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 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 """ }