#!/usr/bin/env nextflow

/*
----------------------------------------------------------------------------------------
    cpipes/centriflaken
----------------------------------------------------------------------------------------
    NAME          : CPIPES
    DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
    GITLAB        : https://xxxxxxxxxx.fda.gov/cfsan-dev/cpipes
    JIRA          : https://xxxxxxxxxx.fda.gov/jira/projects/CPIPES/
    CONTRIBUTORS  : Kranti.Konganti@fda.hhs.gov
----------------------------------------------------------------------------------------
*/

// Enable DSL 2
nextflow.enable.dsl = 2

// Default routines for MAIN
include { pipelineBanner; stopNow; } from "${params.routines}"

// Our banner for CPIPES
log.info pipelineBanner()

switch ("${params.pipeline}") {
    case "nanofactory":
        include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    case "centriflaken":
        include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    case "centriflaken_hy":
        include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    case "spades_only":
        include { SPADES_ONLY } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    default:
        stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken")
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {
    switch ("${params.pipeline}") {
        case "nanofactory":
            NANOFACTORY()
            break
        case "centriflaken":
            CENTRIFLAKEN()
            break
        case "centriflaken_hy":
            CENTRIFLAKEN_HY()
            break
        case "spades_only":
            SPADES_ONLY()
            break
    }
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/