kkonganti@1: #!/usr/bin/env nextflow
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ----------------------------------------------------------------------------------------
kkonganti@1:     cfsan/cpipes
kkonganti@1: ----------------------------------------------------------------------------------------
kkonganti@1:     NAME          : CPIPES
kkonganti@1:     DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@1:     GITLAB        : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
kkonganti@1:     JIRA          : https://xxxxxxxxxx/jira/projects/CPIPES/
kkonganti@1:     CONTRIBUTORS  : Kranti Konganti
kkonganti@1: ----------------------------------------------------------------------------------------
kkonganti@1: */
kkonganti@1: 
kkonganti@1: // Enable DSL 2
kkonganti@1: nextflow.enable.dsl = 2
kkonganti@1: 
kkonganti@1: // Enable local scope of scripts inside modules' directory
kkonganti@1: // Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
kkonganti@1: // is solved.
kkonganti@1: //
kkonganti@1: // nextflow.enable.moduleBinaries = true
kkonganti@1: 
kkonganti@1: // Default routines for MAIN
kkonganti@1: include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@1: 
kkonganti@1: // Our banner for CPIPES
kkonganti@1: log.info pipelineBanner()
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     INCLUDE ALL WORKFLOWS
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: switch ("${params.pipeline}") {
kkonganti@1:     case "bettercallsal":
kkonganti@1:         include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@1:         break
kkonganti@1:     case "bettercallsal_db":
kkonganti@1:         include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@1:         break
kkonganti@1:     default:
kkonganti@1:         stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
kkonganti@1: }
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     RUN ALL WORKFLOWS
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */
kkonganti@1: 
kkonganti@1: workflow {
kkonganti@1:     switch ("${params.pipeline}") {
kkonganti@1:         case "bettercallsal":
kkonganti@1:             BETTERCALLSAL()
kkonganti@1:             break
kkonganti@1:         case "bettercallsal_db":
kkonganti@1:             BETTERCALLSAL_DB()
kkonganti@1:             break
kkonganti@1:     }
kkonganti@1: }
kkonganti@1: 
kkonganti@1: /*
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1:     THE END
kkonganti@1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@1: */