process METHYLDACKEL_EXTRACT { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : 'quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0' }" input: tuple val(meta), path(bam), path(bai) path fasta path fai output: tuple val(meta), path("*.bedGraph"), emit: bedgraph path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ MethylDackel extract \\ $args \\ $fasta \\ $bam cat <<-END_VERSIONS > versions.yml "${task.process}": methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") END_VERSIONS """ }