main.nf

params.bams

// mosdepth is going to need a prefix, a bam, and its index
bams_ch = Channel
    // grab the bams and/or crams
    .fromPath(params.bams, checkIfExists: true)
    // set the first element to the basename of the file without its extension
    // the second element to the alignments (bam or cram)
    // and the third element to the index
    .map { file -> tuple(file.baseName, file, file + ("${file}".endsWith('.cram') ? '.crai' : '.bai')) }

process mosdepth {
    publishDir "./results"
    cpus 3
    memory 4.GB
    time '12h'
    container 'quay.io/biocontainers/mosdepth:0.2.6--hfb13731_0'

    input:
    set sample, file(bam), file(bai) from bams_ch

    output:
    file("${sample}.mosdepth.summary.txt")
    
    script:
    """
    mosdepth -n -t 3 ${sample} $bam
    """
}