Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.0/cpipes @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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100:9d9537c907bd 101:ce6d9548fe89
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/cfsan-dev/cpipes
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 "nanofactory":
34 include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}"
35 break
36 case "centriflaken":
37 include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}"
38 break
39 case "centriflaken_hy":
40 include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}"
41 break
42 default:
43 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken")
44 }
45
46 /*
47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
48 RUN ALL WORKFLOWS
49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
50 */
51
52 workflow {
53 // THIS IS REPETETIVE BUT WE ARE NOT ALLOWED TO INCLUDE "INCLUDE"
54 // INSIDE WORKFLOW
55 switch ("${params.pipeline}") {
56 case "nanofactory":
57 NANOFACTORY()
58 break
59 case "centriflaken":
60 CENTRIFLAKEN()
61 break
62 case "centriflaken_hy":
63 CENTRIFLAKEN_HY()
64 break
65 }
66 }
67
68 /*
69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 THE END
71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
72 */