Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/cpipes @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
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}${params.pipeline}"
39 break
40 case "bettercallsal_lr":
41 include { BETTERCALLSAL_LR } from "${params.workflows}${params.fs}${params.pipeline}"
42 break
43 case "bettercallsal_db":
44 include { BETTERCALLSAL_DB } from "${params.workflows}${params.fs}${params.pipeline}"
45 break
46 default:
47 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline bettercallsal")
48 }
49
50 /*
51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
52 RUN ALL WORKFLOWS
53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
54 */
55
56 workflow {
57 switch ("${params.pipeline}") {
58 case "bettercallsal":
59 BETTERCALLSAL()
60 break
61 case "bettercallsal_lr":
62 BETTERCALLSAL_LR()
63 break
64 case "bettercallsal_db":
65 BETTERCALLSAL_DB()
66 break
67 }
68 }
69
70 /*
71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 THE END
73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
74 */