Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/cpipes @ 10:74ac6f6a9526 tip
planemo upload
| author | kkonganti |
|---|---|
| date | Tue, 01 Apr 2025 11:08:01 -0400 |
| parents | 97cd2f532efe |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 #!/usr/bin/env nextflow |
| kkonganti@0 | 2 |
| kkonganti@0 | 3 /* |
| kkonganti@0 | 4 ---------------------------------------------------------------------------------------- |
| kkonganti@0 | 5 cfsan-dev/cpipes |
| kkonganti@0 | 6 ---------------------------------------------------------------------------------------- |
| kkonganti@0 | 7 NAME : CPIPES |
| kkonganti@0 | 8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA. |
| kkonganti@0 | 9 GITLAB : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework |
| kkonganti@0 | 10 JIRA : https://xxxxxxxxxx/jira/projects/CPIPES/ |
| kkonganti@0 | 11 CONTRIBUTORS : Kranti Konganti |
| kkonganti@0 | 12 ---------------------------------------------------------------------------------------- |
| kkonganti@0 | 13 */ |
| kkonganti@0 | 14 |
| kkonganti@0 | 15 // Enable DSL 2 |
| kkonganti@0 | 16 nextflow.enable.dsl = 2 |
| kkonganti@0 | 17 |
| kkonganti@0 | 18 // Default routines for MAIN |
| kkonganti@0 | 19 include { pipelineBanner; stopNow; } from "${params.routines}" |
| kkonganti@0 | 20 |
| kkonganti@0 | 21 // Our banner for CPIPES |
| kkonganti@0 | 22 log.info pipelineBanner() |
| kkonganti@0 | 23 |
| kkonganti@0 | 24 /* |
| kkonganti@0 | 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| kkonganti@0 | 26 INCLUDE ALL WORKFLOWS |
| kkonganti@0 | 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| kkonganti@0 | 28 */ |
| kkonganti@0 | 29 |
| kkonganti@0 | 30 switch ("${params.pipeline}") { |
| kkonganti@0 | 31 case "nowayout": |
| kkonganti@0 | 32 include { NOWAYOUT } from "${params.workflows}${params.fs}${params.pipeline}" |
| kkonganti@0 | 33 break |
| kkonganti@0 | 34 default: |
| kkonganti@0 | 35 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline nowayout") |
| kkonganti@0 | 36 } |
| kkonganti@0 | 37 |
| kkonganti@0 | 38 /* |
| kkonganti@0 | 39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| kkonganti@0 | 40 RUN ALL WORKFLOWS |
| kkonganti@0 | 41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| kkonganti@0 | 42 */ |
| kkonganti@0 | 43 |
| kkonganti@0 | 44 workflow { |
| kkonganti@0 | 45 // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE" |
| kkonganti@0 | 46 // INSIDE WORKFLOW |
| kkonganti@0 | 47 switch ("${params.pipeline}") { |
| kkonganti@0 | 48 case "nowayout": |
| kkonganti@0 | 49 NOWAYOUT() |
| kkonganti@0 | 50 break |
| kkonganti@0 | 51 } |
| kkonganti@0 | 52 } |
| kkonganti@0 | 53 |
| kkonganti@0 | 54 /* |
| kkonganti@0 | 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| kkonganti@0 | 56 THE END |
| kkonganti@0 | 57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| kkonganti@0 | 58 */ |