wsubworflows.nf

// params defaults
params.help = false
params.cpus = 1
params.C = 'true'

def helpMessage() {
    log.info"""
    Pipeline to align FASTQ file/s to a reference file
    --------------------------------------------------
    Usage:
        nextflow analysis_umi_dsa.nf --cmd aln'
        Options:
            --help	Show this message and exit.
            --cmd  Subworkflow to be executed: Valid subworflows are: ['aln', 'cov', 'dsa'].
    """
}

if (params.help){
    helpMessage()
    exit 0
}

log.info 'Starting the process.....'

// check mandatory parameters
if (!params.cmd) exit 1, 'Please specify a valid cmd'

// Check input path parameters to see if they exist
checkPathParamList = [
    params.ifile, params.reference
]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }

workflow alignment {
    take: value_list
    main:
        fastqc=FASTQC(value_list, params.cpus, params.outdir)
}

workflow {
    main:
        alignment(value_list)
}