cpipes

#!/usr/bin/env nextflow

/*
----------------------------------------------------------------------------------------
    cfsan/cpipes
----------------------------------------------------------------------------------------
    NAME          : CPIPES
    DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
    GITLAB        : https://xxxxxxxxx.fda.gov/Kranti.Konganti/cpipes-framework
    JIRA          : https://xxxxxxxxx.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 ("${params.pipeline}") {
    case "cronology":
        include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    case "cronology_db":
        include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    default:
        stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology")
}

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

workflow {
    switch ("${params.pipeline}") {
        case "cronology":
            CRONOLOGY()
            break
        case "cronology_db":
            CRONOLOGY_DB()
            break
    }
}

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