-
Notifications
You must be signed in to change notification settings - Fork 7
/
main.nf
121 lines (105 loc) · 4.06 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
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/variantbenchmarking
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/variantbenchmarking
Website: https://nf-co.re/variantbenchmarking
Slack : https://nfcore.slack.com/channels/variantbenchmarking
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_variantbenchmarking_pipeline'
params.fasta = getGenomeAttribute('fasta')
params.fai = getGenomeAttribute('fai')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TRUTH PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { getTruthAttribute } from './subworkflows/local/utils_nfcore_variantbenchmarking_pipeline'
params.truth_small = getTruthAttribute('truth_small')
params.high_conf_small = getTruthAttribute('high_conf_small')
params.truth_sv = getTruthAttribute('truth_sv')
params.high_conf_sv = getTruthAttribute('high_conf_sv')
params.truth_cnv = getTruthAttribute('truth_cnv')
params.high_conf_cnv = getTruthAttribute('high_conf_cnv')
params.truth_snv = getTruthAttribute('truth_snv')
params.high_conf_snv = getTruthAttribute('high_conf_snv')
params.truth_indel = getTruthAttribute('truth_indel')
params.high_conf_indel = getTruthAttribute('high_conf_indel')
params.chain = getTruthAttribute('chain')
params.rename_chr = getTruthAttribute('rename_chr')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { VARIANTBENCHMARKING } from './workflows/variantbenchmarking'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_variantbenchmarking_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_variantbenchmarking_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// WORKFLOW: Run main nf-core/sarek analysis pipeline
workflow NFCORE_VARIANTBENCHMARKING {
take:
ch_samplesheet
main:
//
// WORKFLOW: Run pipeline
//
VARIANTBENCHMARKING(
ch_samplesheet
)
emit:
multiqc_report = VARIANTBENCHMARKING.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
)
//
// WORKFLOW: Run main workflow
//
NFCORE_VARIANTBENCHMARKING (
PIPELINE_INITIALISATION.out.samplesheet
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
NFCORE_VARIANTBENCHMARKING.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/