|
0
|
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 */
|
