kkonganti@0: #!/usr/bin/env nextflow
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ----------------------------------------------------------------------------------------
kkonganti@0:     cfsan-dev/cpipes
kkonganti@0: ----------------------------------------------------------------------------------------
kkonganti@0:     NAME          : CPIPES
kkonganti@0:     DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@0:     GITLAB        : https://cfsan-git.fda.gov/Kranti.Konganti/cpipes-framework
kkonganti@0:     JIRA          : https://sde.fda.gov/jira/projects/CPIPES/
kkonganti@0:     CONTRIBUTORS  : Kranti.Konganti@fda.hhs.gov
kkonganti@0: ----------------------------------------------------------------------------------------
kkonganti@0: */
kkonganti@0: 
kkonganti@0: // Enable DSL 2
kkonganti@0: nextflow.enable.dsl = 2
kkonganti@0: 
kkonganti@0: // Default routines for MAIN
kkonganti@0: include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@0: 
kkonganti@0: // Our banner for CPIPES
kkonganti@0: log.info pipelineBanner()
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     NAMED WORKFLOW CAN BE USED TO RUN A SPECIFIC PIPELINE. THIS IS THE RECOMMENDED WAY. 
kkonganti@0:     NEED TO FIND A BETTER SOLUTION IF WE SEE A LOT OF PIPELINES.
kkonganti@0:     See: https://github.com/nf-core/rnaseq/issues/619
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: switch ("${params.pipeline}") {
kkonganti@0:     case "cronology":
kkonganti@0:         include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@0:         break
kkonganti@0:     case "cronology_db":
kkonganti@0:         include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@0:         break
kkonganti@0:     default:
kkonganti@0:         stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology")
kkonganti@0: }
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     RUN ALL WORKFLOWS
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */
kkonganti@0: 
kkonganti@0: workflow {
kkonganti@0:     // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
kkonganti@0:     // INSIDE WORKFLOW
kkonganti@0:     switch ("${params.pipeline}") {
kkonganti@0:         case "cronology":
kkonganti@0:             CRONOLOGY()
kkonganti@0:             break
kkonganti@0:         case "cronology_db":
kkonganti@0:             CRONOLOGY_DB()
kkonganti@0:             break
kkonganti@0:     }
kkonganti@0: }
kkonganti@0: 
kkonganti@0: /*
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0:     THE END
kkonganti@0: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@0: */