/
germline_detect_variants.cwl
129 lines (127 loc) · 3.38 KB
/
germline_detect_variants.cwl
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
122
123
124
125
126
127
128
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment and germline variant detection"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference:
type: string
cram:
type: File
emit_reference_confidence:
type: string
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
contamination_fraction:
type: string?
vep_cache_dir:
type: string
synonyms_file:
type: File?
coding_only:
type: boolean?
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
limit_variant_intervals:
type: File
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
outputs:
gvcf:
type: File[]
outputSource: haplotype_caller/gvcf
final_vcf:
type: File
outputSource: index_annotated_vcf/indexed_vcf
secondaryFiles: [.tbi]
coding_vcf:
type: File
outputSource: index_coding_vcf/indexed_vcf
secondaryFiles: [.tbi]
limited_vcf:
type: File
outputSource: limit_variants/filtered_vcf
secondaryFiles: [.tbi]
vep_summary:
type: File
outputSource: annotate_variants/vep_summary
steps:
haplotype_caller:
run: gatk_haplotypecaller_iterator.cwl
in:
reference: reference
cram: cram
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
contamination_fraction: contamination_fraction
out:
[gvcf]
genotype_gvcfs:
run: ../tools/gatk_genotypegvcfs.cwl
in:
reference: reference
gvcfs: haplotype_caller/gvcf
out:
[genotype_vcf]
annotate_variants:
run: ../tools/vep.cwl
in:
vcf: genotype_gvcfs/genotype_vcf
cache_dir: vep_cache_dir
synonyms_file: synonyms_file
coding_only: coding_only
reference: reference
custom_gnomad_vcf: custom_gnomad_vcf
custom_clinvar_vcf: custom_clinvar_vcf
out:
[annotated_vcf, vep_summary]
bgzip_annotated_vcf:
run: ../tools/bgzip.cwl
in:
file: annotate_variants/annotated_vcf
out:
[bgzipped_file]
index_annotated_vcf:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip_annotated_vcf/bgzipped_file
out:
[indexed_vcf]
coding_variant_filter:
run: ../tools/filter_vcf_coding_variant.cwl
in:
vcf: annotate_variants/annotated_vcf
out:
[filtered_vcf]
bgzip_coding_vcf:
run: ../tools/bgzip.cwl
in:
file: coding_variant_filter/filtered_vcf
out:
[bgzipped_file]
index_coding_vcf:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip_coding_vcf/bgzipped_file
out:
[indexed_vcf]
limit_variants:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: index_coding_vcf/indexed_vcf
interval_list: limit_variant_intervals
exclude_filtered:
default: true
out:
[filtered_vcf]