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comparison 0.2.0/cpipes @ 0:9e8b1c747a6a draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
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://xxxxxxxxx.fda.gov/Kranti.Konganti/cpipes-framework
10 JIRA : https://xxxxxxxxx.fda.gov/jira/projects/CPIPES/
11 CONTRIBUTORS : Kranti.Konganti@fda.hhs.gov
12 ----------------------------------------------------------------------------------------
13 */
14
15 // Enable DSL 2
16 nextflow.enable.dsl = 2
17
18 // Default routines for MAIN
19 include { pipelineBanner; stopNow; } from "${params.routines}"
20
21 // Our banner for CPIPES
22 log.info pipelineBanner()
23
24 switch ("${params.pipeline}") {
25 case "cronology":
26 include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}"
27 break
28 case "cronology_db":
29 include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}"
30 break
31 default:
32 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology")
33 }
34
35 /*
36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 RUN ALL WORKFLOWS
38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 */
40
41 workflow {
42 switch ("${params.pipeline}") {
43 case "cronology":
44 CRONOLOGY()
45 break
46 case "cronology_db":
47 CRONOLOGY_DB()
48 break
49 }
50 }
51
52 /*
53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
54 THE END
55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
56 */