// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process BISMARK_SUMMARY {
    label 'process_low'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

    conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
    } else {
        container "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

    script:
    """
    bismark2summary

    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        ${getSoftwareName(task.process)}: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
    END_VERSIONS
    """
}