cpipes

#!/usr/bin/env nextflow

/*
----------------------------------------------------------------------------------------
    cfsan/cpipes
----------------------------------------------------------------------------------------
    NAME          : CPIPES
    DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
    GITLAB        : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
    JIRA          : https://xxxxxxxxxx/jira/projects/CPIPES/
    CONTRIBUTORS  : Kranti Konganti
----------------------------------------------------------------------------------------
*/

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

// Enable local scope of scripts inside modules' directory
// Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
// is solved.
//
// nextflow.enable.moduleBinaries = true

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

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

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    INCLUDE ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

switch ("${params.pipeline}") {
    case "bettercallsal":
        include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    case "bettercallsal_lr":
        include { BETTERCALLSAL_LR } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    case "bettercallsal_db":
        include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
        break
    default:
        stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
}

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

workflow {
    switch ("${params.pipeline}") {
        case "bettercallsal":
            BETTERCALLSAL()
            break
        case "bettercallsal_lr":
            BETTERCALLSAL_LR()
            break
        case "bettercallsal_db":
            BETTERCALLSAL_DB()
            break
    }
}

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