main.nf

include { ingest } from './subworkflows/ingest'
include { classify_novel_viruses } from './modules/classify_novel_viruses'
include { process_run } from './subworkflows/process_run'

workflow {
    if (params.output)
    	exit 1, "Please specify outdir with --outdir -- aborting"
    if (params.out_dir)
        exit 1, "Please specify outdir with --outdir -- aborting"

    unique_id = "${params.unique_id}"

    if (unique_id == "null") {
        if (params.fastq) {
            fastq = file(params.fastq, type: "file", checkIfExists:true)
            unique_id = "${fastq.simpleName}"
        } else if (params.fastq_dir) {
            fastq_dir = file(params.fastq_dir, type: "dir", checkIfExists:true)
            unique_id = "${fastq_dir.simpleName}"
        } else if (params.paired && params.fastq1 && params.fastq2) {
            fastq1 = file(params.fastq1, type: "file", checkIfExists:true)
            unique_id = "${fastq1.simpleName}"
        } else if (params.run_dir) {
            run_dir = file(params.run_dir, type: "dir", checkIfExists:true)
            unique_id = "${run_dir.simpleName}"
        } else {
            exit 1, "One of fastq, fastq_dir or fastq1 and fastq2 need to be provided -- aborting"
        }
    }

    // check input fastq exists and run fastp
    if (params.run_dir)
        process_run(unique_id)
    else if (params.classify_novel_viruses)
        classify_novel_viruses(unique_id)
    else
        ingest(unique_id)
}