kkonganti@17: #!/usr/bin/env nextflow
kkonganti@17: 
kkonganti@17: /*
kkonganti@17: ----------------------------------------------------------------------------------------
kkonganti@17:     cfsan/cpipes
kkonganti@17: ----------------------------------------------------------------------------------------
kkonganti@17:     NAME          : CPIPES
kkonganti@17:     DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@17:     GITLAB        : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
kkonganti@17:     JIRA          : https://xxxxxxxxxx/jira/projects/CPIPES/
kkonganti@17:     CONTRIBUTORS  : Kranti Konganti
kkonganti@17: ----------------------------------------------------------------------------------------
kkonganti@17: */
kkonganti@17: 
kkonganti@17: // Enable DSL 2
kkonganti@17: nextflow.enable.dsl = 2
kkonganti@17: 
kkonganti@17: // Enable local scope of scripts inside modules' directory
kkonganti@17: // Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
kkonganti@17: // is solved.
kkonganti@17: //
kkonganti@17: // nextflow.enable.moduleBinaries = true
kkonganti@17: 
kkonganti@17: // Default routines for MAIN
kkonganti@17: include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@17: 
kkonganti@17: // Our banner for CPIPES
kkonganti@17: log.info pipelineBanner()
kkonganti@17: 
kkonganti@17: /*
kkonganti@17: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17:     INCLUDE ALL WORKFLOWS
kkonganti@17: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17: */
kkonganti@17: 
kkonganti@17: switch ("${params.pipeline}") {
kkonganti@17:     case "bettercallsal":
kkonganti@17:         include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@17:         break
kkonganti@17:     case "bettercallsal_db":
kkonganti@17:         include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@17:         break
kkonganti@17:     default:
kkonganti@17:         stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
kkonganti@17: }
kkonganti@17: 
kkonganti@17: /*
kkonganti@17: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17:     RUN ALL WORKFLOWS
kkonganti@17: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17: */
kkonganti@17: 
kkonganti@17: workflow {
kkonganti@17:     switch ("${params.pipeline}") {
kkonganti@17:         case "bettercallsal":
kkonganti@17:             BETTERCALLSAL()
kkonganti@17:             break
kkonganti@17:         case "bettercallsal_db":
kkonganti@17:             BETTERCALLSAL_DB()
kkonganti@17:             break
kkonganti@17:     }
kkonganti@17: }
kkonganti@17: 
kkonganti@17: /*
kkonganti@17: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17:     THE END
kkonganti@17: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17: */