Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.1.0/cpipes @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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-1:000000000000 0:c8597e9e1a97
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://cfsan-git.fda.gov/Kranti.Konganti/cpipes-framework
10 JIRA : https://sde.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 "${params.routines}"
20
21 // Our banner for CPIPES
22 log.info pipelineBanner()
23
24 /*
25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
26 NAMED WORKFLOW CAN BE USED TO RUN A SPECIFIC PIPELINE. THIS IS THE RECOMMENDED WAY.
27 NEED TO FIND A BETTER SOLUTION IF WE SEE A LOT OF PIPELINES.
28 See: https://github.com/nf-core/rnaseq/issues/619
29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
30 */
31
32 switch ("${params.pipeline}") {
33 case "cronology":
34 include { CRONOLOGY } from "${params.workflows}${params.fs}${params.pipeline}"
35 break
36 case "cronology_db":
37 include { CRONOLOGY_DB } from "${params.workflows}${params.fs}${params.pipeline}"
38 break
39 default:
40 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline cronology")
41 }
42
43 /*
44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
45 RUN ALL WORKFLOWS
46 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
47 */
48
49 workflow {
50 // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
51 // INSIDE WORKFLOW
52 switch ("${params.pipeline}") {
53 case "cronology":
54 CRONOLOGY()
55 break
56 case "cronology_db":
57 CRONOLOGY_DB()
58 break
59 }
60 }
61
62 /*
63 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
64 THE END
65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
66 */