Mercurial > repos > kkonganti > hfp_nowayout

comparison 0.5.0/cpipes @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 #!/usr/bin/env nextflow
2
3 /*
4 ----------------------------------------------------------------------------------------
5 cfsan-dev/cpipes
6 ----------------------------------------------------------------------------------------
7 NAME : CPIPES
8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA.
9 GITLAB : https://xxxxxxxxxx/Kranti.Konganti/cpipes-framework
10 JIRA : https://xxxxxxxxxx/jira/projects/CPIPES/
11 CONTRIBUTORS : Kranti Konganti
12 ----------------------------------------------------------------------------------------
13 */
14
15 // Enable DSL 2
16 nextflow.enable.dsl = 2
17
18 // Default routines for MAIN
19 include { pipelineBanner; stopNow; } from "${params.routines}"
20
21 // Our banner for CPIPES
22 log.info pipelineBanner()
23
24 /*
25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
26 INCLUDE ALL WORKFLOWS
27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
28 */
29
30 switch ("${params.pipeline}") {
31 case "nowayout":
32 include { NOWAYOUT } from "${params.workflows}${params.fs}${params.pipeline}"
33 break
34 default:
35 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline nowayout")
36 }
37
38 /*
39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 RUN ALL WORKFLOWS
41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
42 */
43
44 workflow {
45 // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
46 // INSIDE WORKFLOW
47 switch ("${params.pipeline}") {
48 case "nowayout":
49 NOWAYOUT()
50 break
51 }
52 }
53
54 /*
55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 THE END
57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
58 */