process BISMARK_METHYLATIONEXTRACTOR { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : 'quay.io/biocontainers/bismark:0.23.0--0' }" input: tuple val(meta), path(bam) path index output: tuple val(meta), path("*.bedGraph.gz") , emit: bedgraph tuple val(meta), path("*.txt.gz") , emit: methylation_calls tuple val(meta), path("*.cov.gz") , emit: coverage tuple val(meta), path("*_splitting_report.txt"), emit: report tuple val(meta), path("*.M-bias.txt") , emit: mbias path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def seqtype = meta.single_end ? '-s' : '-p' """ bismark_methylation_extractor \\ --bedGraph \\ --counts \\ --gzip \\ --report \\ $seqtype \\ $args \\ $bam cat <<-END_VERSIONS > versions.yml "${task.process}": bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ }