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 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 """ }