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://xxxxxxxxx.fda.gov/Kranti.Konganti/cpipes-framework
kkonganti@11:     JIRA          : https://xxxxxxxxx.fda.gov/jira/projects/CPIPES/
kkonganti@11:     CONTRIBUTORS  : Kranti.Konganti@fda.hhs.gov
kkonganti@11: ----------------------------------------------------------------------------------------
kkonganti@11: */
kkonganti@11: 
kkonganti@11: // Enable DSL 2
kkonganti@11: nextflow.enable.dsl = 2
kkonganti@11: 
kkonganti@11: // Default routines for MAIN
kkonganti@11: include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@11: 
kkonganti@11: // Our banner for CPIPES
kkonganti@11: log.info pipelineBanner()
kkonganti@11: 
kkonganti@11: switch ("${params.pipeline}") {
kkonganti@11:     case "cronology":
kkonganti@11:         include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@11:         break
kkonganti@11:     case "cronology_db":
kkonganti@11:         include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@11:         break
kkonganti@11:     default:
kkonganti@11:         stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology")
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 "cronology":
kkonganti@11:             CRONOLOGY()
kkonganti@11:             break
kkonganti@11:         case "cronology_db":
kkonganti@11:             CRONOLOGY_DB()
kkonganti@11:             break
kkonganti@11:     }
kkonganti@11: }
kkonganti@11: 
kkonganti@11: /*
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11:     THE END
kkonganti@11: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11: */