kkonganti@11: #!/usr/bin/env nextflow
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ----------------------------------------------------------------------------------------
kkonganti@11:     cfsan/cpipes
kkonganti@11: ----------------------------------------------------------------------------------------
kkonganti@11:     NAME          : CPIPES
kkonganti@11:     DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@11:     GITLAB        : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
kkonganti@11:     JIRA          : https://xxxxxxxxxx/jira/projects/CPIPES/
kkonganti@11:     CONTRIBUTORS  : Kranti Konganti
kkonganti@11: ----------------------------------------------------------------------------------------
kkonganti@11: */
kkonganti@11: 
kkonganti@11: // Enable DSL 2
kkonganti@11: nextflow.enable.dsl = 2
kkonganti@11: 
kkonganti@11: // Enable local scope of scripts inside modules' directory
kkonganti@11: // Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
kkonganti@11: // is solved.
kkonganti@11: //
kkonganti@11: // nextflow.enable.moduleBinaries = true
kkonganti@11: 
kkonganti@11: // Default routines for MAIN
kkonganti@11: include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@11: 
kkonganti@11: // Our banner for CPIPES
kkonganti@11: log.info pipelineBanner()
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     INCLUDE ALL WORKFLOWS
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: switch ("${params.pipeline}") {
kkonganti@11:     case "bettercallsal":
kkonganti@11:         include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@11:         break
kkonganti@11:     case "bettercallsal_db":
kkonganti@11:         include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@11:         break
kkonganti@11:     default:
kkonganti@11:         stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     RUN ALL WORKFLOWS
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */
kkonganti@11: 
kkonganti@11: workflow {
kkonganti@11:     switch ("${params.pipeline}") {
kkonganti@11:         case "bettercallsal":
kkonganti@11:             BETTERCALLSAL()
kkonganti@11:             break
kkonganti@11:         case "bettercallsal_db":
kkonganti@11:             BETTERCALLSAL_DB()
kkonganti@11:             break
kkonganti@11:     }
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     THE END
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */