process BISMARK_SUMMARY { label 'process_low' conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' : 'quay.io/biocontainers/bismark:0.23.0--0' }" input: path(bam) path(align_report) path(dedup_report) path(splitting_report) path(mbias) output: path "*report.{html,txt}", emit: summary path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' """ bismark2summary cat <<-END_VERSIONS > versions.yml "${task.process}": bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ }