Caluclate deduplication rate

[priesgo]

Do something like this

process DUPLICATION_RATE {
    cpus params.cpus
    memory params.memory
    tag "${name}"
    //publishDir "${params.output}/${name}/metrics/coverage", mode: "copy"
    //publishDir "${params.output}/${name}/", mode: "copy", pattern: "software_versions.*"

    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)

    input:
        tuple val(name), file(bam), file(bai)

    output:
        file("${name}.duplication_rate.tsv")
        
    script:
    """
    samtools flagstat -@ ${task.cpus} ${bam} > output.txt
    parse_duplication_rate.py output.txt 
    """
}