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author kkonganti
date Mon, 15 Jul 2024 21:40:42 -0400
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kkonganti@11 1 #!/usr/bin/env nextflow
kkonganti@11 2
kkonganti@11 3 /*
kkonganti@11 4 ----------------------------------------------------------------------------------------
kkonganti@11 5 cfsan/cpipes
kkonganti@11 6 ----------------------------------------------------------------------------------------
kkonganti@11 7 NAME : CPIPES
kkonganti@11 8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@11 9 GITLAB : https://xxxxxxxxx.fda.gov/Kranti.Konganti/cpipes-framework
kkonganti@11 10 JIRA : https://xxxxxxxxx.fda.gov/jira/projects/CPIPES/
kkonganti@11 11 CONTRIBUTORS : Kranti.Konganti@fda.hhs.gov
kkonganti@11 12 ----------------------------------------------------------------------------------------
kkonganti@11 13 */
kkonganti@11 14
kkonganti@11 15 // Enable DSL 2
kkonganti@11 16 nextflow.enable.dsl = 2
kkonganti@11 17
kkonganti@11 18 // Default routines for MAIN
kkonganti@11 19 include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@11 20
kkonganti@11 21 // Our banner for CPIPES
kkonganti@11 22 log.info pipelineBanner()
kkonganti@11 23
kkonganti@11 24 switch ("${params.pipeline}") {
kkonganti@11 25 case "cronology":
kkonganti@11 26 include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@11 27 break
kkonganti@11 28 case "cronology_db":
kkonganti@11 29 include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@11 30 break
kkonganti@11 31 default:
kkonganti@11 32 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology")
kkonganti@11 33 }
kkonganti@11 34
kkonganti@11 35 /*
kkonganti@11 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11 37 RUN ALL WORKFLOWS
kkonganti@11 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11 39 */
kkonganti@11 40
kkonganti@11 41 workflow {
kkonganti@11 42 switch ("${params.pipeline}") {
kkonganti@11 43 case "cronology":
kkonganti@11 44 CRONOLOGY()
kkonganti@11 45 break
kkonganti@11 46 case "cronology_db":
kkonganti@11 47 CRONOLOGY_DB()
kkonganti@11 48 break
kkonganti@11 49 }
kkonganti@11 50 }
kkonganti@11 51
kkonganti@11 52 /*
kkonganti@11 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11 54 THE END
kkonganti@11 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@11 56 */