Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/cpipes @ 0:082e0091e813 draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 #!/usr/bin/env nextflow
2
3 /*
4 ----------------------------------------------------------------------------------------
5 cpipes/centriflaken
6 ----------------------------------------------------------------------------------------
7 NAME : CPIPES
8 DESCRIPTION : Modular Nextflow pipelines at CFSAN, FDA.
9 GITLAB : https://xxxxxxxxxx.fda.gov/cfsan-dev/cpipes
10 JIRA : https://xxxxxxxxxx.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 "nanofactory":
26 include { NANOFACTORY } from "${params.workflows}${params.fs}${params.pipeline}"
27 break
28 case "centriflaken":
29 include { CENTRIFLAKEN } from "${params.workflows}${params.fs}${params.pipeline}"
30 break
31 case "centriflaken_hy":
32 include { CENTRIFLAKEN_HY } from "${params.workflows}${params.fs}${params.pipeline}"
33 break
34 case "spades_only":
35 include { SPADES_ONLY } from "${params.workflows}${params.fs}${params.pipeline}"
36 break
37 default:
38 stopNow("PLEASE MENTION A PIPELINE NAME. Ex: --pipeline centriflaken")
39 }
40
41 /*
42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
43 RUN ALL WORKFLOWS
44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
45 */
46
47 workflow {
48 switch ("${params.pipeline}") {
49 case "nanofactory":
50 NANOFACTORY()
51 break
52 case "centriflaken":
53 CENTRIFLAKEN()
54 break
55 case "centriflaken_hy":
56 CENTRIFLAKEN_HY()
57 break
58 case "spades_only":
59 SPADES_ONLY()
60 break
61 }
62 }
63
64 /*
65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
66 THE END
67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
68 */