Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/cpipes @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 #!/usr/bin/env nextflow
2
3 /*
4 ----------------------------------------------------------------------------------------
5 cfsan/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 // Enable local scope of scripts inside modules' directory
19 // Buggy. To be enabled after github.com/nextflow-io/nextflow/issues/3308
20 // is solved.
21 //
22 // nextflow.enable.moduleBinaries = true
23
24 // Default routines for MAIN
25 include { pipelineBanner; stopNow; } from "${params.routines}"
26
27 // Our banner for CPIPES
28 log.info pipelineBanner()
29
30 /*
31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 INCLUDE ALL WORKFLOWS
33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 */
35
36 switch ("${params.pipeline}") {
37 case "bettercallsal":
38 include { BETTERCALLSAL } from "${params.workflows}${params.fs}${params.pipeline}"
39 break
40 case "bettercallsal_db":
41 include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
42 break
43 default:
44 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
45 }
46
47 /*
48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
49 RUN ALL WORKFLOWS
50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
51 */
52
53 workflow {
54 switch ("${params.pipeline}") {
55 case "bettercallsal":
56 BETTERCALLSAL()
57 break
58 case "bettercallsal_db":
59 BETTERCALLSAL_DB()
60 break
61 }
62 }
63
64 /*
65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
66 THE END
67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 */