forked from nf-core/raredisease
-
Notifications
You must be signed in to change notification settings - Fork 0
/
main.nf
90 lines (78 loc) · 4.15 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
#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/raredisease
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/raredisease
Website: https://nf-co.re/raredisease
Slack : https://nfcore.slack.com/channels/raredisease
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.fasta_fai = WorkflowMain.getGenomeAttribute(params, 'fai')
params.bwamem2_index = WorkflowMain.getGenomeAttribute(params, 'bwamem2')
params.call_interval = WorkflowMain.getGenomeAttribute(params, 'call_interval')
params.gnomad = WorkflowMain.getGenomeAttribute(params, 'gnomad')
params.gnomad_af = WorkflowMain.getGenomeAttribute(params, 'gnomad_af')
params.gnomad_af_tbi = WorkflowMain.getGenomeAttribute(params, 'gnomad_af_tbi')
params.intervals_mt = WorkflowMain.getGenomeAttribute(params, 'intervals_mt')
params.known_dbsnp = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp')
params.known_dbsnp_tbi = WorkflowMain.getGenomeAttribute(params, 'known_dbsnp_tbi')
params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels')
params.known_mills = WorkflowMain.getGenomeAttribute(params, 'known_mills')
params.ml_model = WorkflowMain.getGenomeAttribute(params, 'ml_model')
params.reduced_penetrance = WorkflowMain.getGenomeAttribute(params, 'reduced_penetrance')
params.score_config_snv = WorkflowMain.getGenomeAttribute(params, 'score_config_snv')
params.score_config_sv = WorkflowMain.getGenomeAttribute(params, 'score_config_sv')
params.target_bed = WorkflowMain.getGenomeAttribute(params, 'target_bed')
params.sentieonbwa_index = WorkflowMain.getGenomeAttribute(params, 'bwa')
params.svdb_query_dbs = WorkflowMain.getGenomeAttribute(params, 'svdb_query_dbs')
params.variant_catalog = WorkflowMain.getGenomeAttribute(params, 'variant_catalog')
params.vep_filters = WorkflowMain.getGenomeAttribute(params, 'vep_filters')
params.vcfanno_resources = WorkflowMain.getGenomeAttribute(params, 'vcfanno_resources')
params.vcfanno_toml = WorkflowMain.getGenomeAttribute(params, 'vcfanno_toml')
params.vep_cache = WorkflowMain.getGenomeAttribute(params, 'vep_cache')
params.gens_interval_list = WorkflowMain.getGenomeAttribute(params, 'gens_interval_list')
params.gens_pon = WorkflowMain.getGenomeAttribute(params, 'gens_pon')
params.gens_gnomad_pos = WorkflowMain.getGenomeAttribute(params, 'gens_gnomad_pos')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
WorkflowMain.initialise(workflow, params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { RAREDISEASE } from './workflows/raredisease'
//
// WORKFLOW: Run main nf-core/raredisease analysis pipeline
//
workflow NFCORE_RAREDISEASE {
RAREDISEASE ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
NFCORE_RAREDISEASE ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/