-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmain.nf
executable file
·103 lines (84 loc) · 3.59 KB
/
main.nf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
UPHL-BioNGS/walkercreek
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/UPHL-BioNGS/walkercreek
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
WorkflowMain.initialise(workflow, params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
if (params.platform == 'flu_illumina') {
include { FLU_ILLUMINA } from './workflows/flu_illumina'
println "Running flu_illumina platform for clinical influenza samples with IRMA: Iterative Refinement Meta-Assembler."
} else if (params.platform == 'flu_ww_illumina') {
include { FLU_WW_ILLUMINA } from './workflows/flu_ww_illumina'
println "Running flu_ww_illumina platform for influenza wastewater samples."
} else if (params.platform == 'flu_nanopore') {
include { FLU_NANOPORE } from './workflows/flu_nanopore'
println "Running flu_nanopore platform for clinical influenza samples with IRMA: Iterative Refinement Meta-Assembler."
} else if (params.platform == 'flu_ww_nanopore') {
include { FLU_WW_NANOPORE } from './workflows/flu_ww_nanopore'
println "Running flu_ww_nanopore platform for wastewater influenza samples with IRMA: Iterative Refinement Meta-Assembler."
} else if (params.platform == 'rsv_illumina') {
include { RSV_ILLUMINA } from './workflows/rsv_illumina'
println "Running rsv_illumina platform for clinical RSV samples with IRMA: Iterative Refinement Meta-Assembler."
} else {
// Default case if none of the options match
println "Unknown platform! Please choose a valid option from --platform flu_illumina, flu_nanopore, flu_ww_illumina, flu_ww_nanopore, or rsv_illumina."
exit 1
}
//
// WORKFLOW: Run main UPHL-BioNGS/walkercreek analysis pipeline
//
workflow NFCORE_WALKERCREEK {
//
// WORKFLOW: Run main UPHL-BioNGS/walkercreek flu_illumina analysis pipeline
//
if (params.platform == 'flu_illumina') {
FLU_ILLUMINA ()
//
// WORKFLOW: Run main UPHL-BioNGS/walkercreek flu_ww_illumina analysis pipeline
//
} else if (params.platform == 'flu_ww_illumina') {
FLU_WW_ILLUMINA ()
//
// WORKFLOW: Run main UPHL-BioNGS/walkercreek flu_nanopore analysis pipeline
//
} else if (params.platform == 'flu_nanopore') {
FLU_NANOPORE ()
//
// WORKFLOW: Run main UPHL-BioNGS/walkercreek flu_ww_nanopore analysis pipeline
//
} else if (params.platform == 'flu_ww_nanopore') {
FLU_WW_NANOPORE ()
//
// WORKFLOW: Run main UPHL-BioNGS/walkercreek rsv_illumina analysis pipeline
//
} else if (params.platform == 'rsv_illumina') {
RSV_ILLUMINA ()
}
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
NFCORE_WALKERCREEK ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/