process {

    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
    withName: "test_fgbio_fastqtobam_paired_cram:FGBIO_FASTQTOBAM" {
        ext.prefix = {"${meta.id}.cram"}
    }
    withName: "test_fgbio_fastqtobam_paired_bam:FGBIO_FASTQTOBAM" {
        ext.prefix = {"${meta.id}.bam"}
    }
    withName: "test_fgbio_fastqtobam_paired_umi:FGBIO_FASTQTOBAM" {
        ext.args = "--read-structures +T 12M11S+T"
    }
    withName: "test_fgbio_fastqtobam_paired_custom_samplename:FGBIO_FASTQTOBAM" {
        ext.args = "--sample CustomSample --library CustomLibrary"
    }
}