kkonganti@92: #!/usr/bin/env nextflow
kkonganti@92: 
kkonganti@92: /*
kkonganti@92: ----------------------------------------------------------------------------------------
kkonganti@92:     cfsan-dev/cpipes
kkonganti@92: ----------------------------------------------------------------------------------------
kkonganti@92:     NAME          : CPIPES
kkonganti@92:     DESCRIPTION   : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@92:     GITLAB        : https://cfsan-git.fda.gov/cfsan-dev/cpipes
kkonganti@92:     JIRA          : https://sde.fda.gov/jira/projects/CPIPES/
kkonganti@92:     CONTRIBUTORS  : Kranti.Konganti@fda.hhs.gov
kkonganti@92: ----------------------------------------------------------------------------------------
kkonganti@92: */
kkonganti@92: 
kkonganti@92: // Enable DSL 2
kkonganti@92: nextflow.enable.dsl = 2
kkonganti@92: 
kkonganti@92: // Default routines for MAIN
kkonganti@92: include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@92: 
kkonganti@92: // Our banner for CPIPES
kkonganti@92: log.info pipelineBanner()
kkonganti@92: 
kkonganti@92: /*
kkonganti@92: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92:     NAMED WORKFLOW CAN BE USED TO RUN A SPECIFIC PIPELINE. THIS IS THE RECOMMENDED WAY. 
kkonganti@92:     NEED TO FIND A BETTER SOLUTION IF WE SEE A LOT OF PIPELINES.
kkonganti@92:     See: https://github.com/nf-core/rnaseq/issues/619
kkonganti@92: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92: */
kkonganti@92: 
kkonganti@92: switch ("${params.pipeline}") {
kkonganti@92:     case "nanofactory":
kkonganti@92:         include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@92:         break
kkonganti@92:     case "centriflaken":
kkonganti@92:         include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@92:         break
kkonganti@92:     case "centriflaken_hy":
kkonganti@92:         include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@92:         break
kkonganti@92:     default:
kkonganti@92:         stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken")
kkonganti@92: }
kkonganti@92: 
kkonganti@92: /*
kkonganti@92: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92:     RUN ALL WORKFLOWS
kkonganti@92: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92: */
kkonganti@92: 
kkonganti@92: workflow {
kkonganti@92:     // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
kkonganti@92:     // INSIDE WORKFLOW
kkonganti@92:     switch ("${params.pipeline}") {
kkonganti@92:         case "nanofactory":
kkonganti@92:             NANOFACTORY()
kkonganti@92:             break
kkonganti@92:         case "centriflaken":
kkonganti@92:             CENTRIFLAKEN()
kkonganti@92:             break
kkonganti@92:         case "centriflaken_hy":
kkonganti@92:             CENTRIFLAKEN_HY()
kkonganti@92:             break
kkonganti@92:     }
kkonganti@92: }
kkonganti@92: 
kkonganti@92: /*
kkonganti@92: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92:     THE END
kkonganti@92: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@92: */