Mercurial > repos > kkonganti > cfsan_bettercallsal

annotate 0.7.0/cpipes @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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kkonganti@17 1 #!/usr/bin/env nextflow
kkonganti@17 2
kkonganti@17 3 /*
kkonganti@17 4 ----------------------------------------------------------------------------------------
kkonganti@17 5 cfsan/cpipes
kkonganti@17 6 ----------------------------------------------------------------------------------------
kkonganti@17 7 NAME : CPIPES
kkonganti@17 8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA.
kkonganti@17 9 GITLAB : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
kkonganti@17 10 JIRA : https://xxxxxxxxxx/jira/projects/CPIPES/
kkonganti@17 11 CONTRIBUTORS : Kranti Konganti
kkonganti@17 12 ----------------------------------------------------------------------------------------
kkonganti@17 13 */
kkonganti@17 14
kkonganti@17 15 // Enable DSL 2
kkonganti@17 16 nextflow.enable.dsl = 2
kkonganti@17 17
kkonganti@17 18 // Enable local scope of scripts inside modules' directory
kkonganti@17 19 // Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
kkonganti@17 20 // is solved.
kkonganti@17 21 //
kkonganti@17 22 // nextflow.enable.moduleBinaries = true
kkonganti@17 23
kkonganti@17 24 // Default routines for MAIN
kkonganti@17 25 include { pipelineBanner; stopNow; } from "${params.routines}"
kkonganti@17 26
kkonganti@17 27 // Our banner for CPIPES
kkonganti@17 28 log.info pipelineBanner()
kkonganti@17 29
kkonganti@17 30 /*
kkonganti@17 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 32 INCLUDE ALL WORKFLOWS
kkonganti@17 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 34 */
kkonganti@17 35
kkonganti@17 36 switch ("${params.pipeline}") {
kkonganti@17 37 case "bettercallsal":
kkonganti@17 38 include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@17 39 break
kkonganti@17 40 case "bettercallsal_db":
kkonganti@17 41 include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
kkonganti@17 42 break
kkonganti@17 43 default:
kkonganti@17 44 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
kkonganti@17 45 }
kkonganti@17 46
kkonganti@17 47 /*
kkonganti@17 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 49 RUN ALL WORKFLOWS
kkonganti@17 50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 51 */
kkonganti@17 52
kkonganti@17 53 workflow {
kkonganti@17 54 switch ("${params.pipeline}") {
kkonganti@17 55 case "bettercallsal":
kkonganti@17 56 BETTERCALLSAL()
kkonganti@17 57 break
kkonganti@17 58 case "bettercallsal_db":
kkonganti@17 59 BETTERCALLSAL_DB()
kkonganti@17 60 break
kkonganti@17 61 }
kkonganti@17 62 }
kkonganti@17 63
kkonganti@17 64 /*
kkonganti@17 65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 66 THE END
kkonganti@17 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@17 68 */