Mercurial > repos > galaxytrakr > hfp_nowayout_awsbatch

comparison 0.5.0/cpipes @ 0:3c767f9cfd88 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:37:56 +0000
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-1:000000000000 0:3c767f9cfd88
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}${params.pipeline}"
33 break
34 default:
35 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline nowayout")
36 }
37
38 /*
39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 RUN ALL WORKFLOWS
41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
42 */
43
44 workflow {
45 switch ("${params.pipeline}") {
46 case "nowayout":
47 NOWAYOUT()
48 break
49 }
50 }
51
52 /*
53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
54 THE END
55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 */