-
Notifications
You must be signed in to change notification settings - Fork 22
/
mc3_vcf_postfilter.cwl
122 lines (112 loc) · 2.2 KB
/
mc3_vcf_postfilter.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
cwlVersion: v1.0
class: Workflow
inputs:
rawRadia:
type: File
rawVarscans:
type: File
rawSomsniper:
type: File
rawMuse:
type: File
rawPindel:
type: File
rawIndelocator:
type: File
tumor:
type: File
normal:
type: File
reference:
type: File
tumorID:
type: string
normalID:
type: string
steps:
filterRadia:
run: ./tools/radia-tool/radia_filter.cwl
in:
inputVCF: rawRadia
tumor: tumor
normal: normal
patientId:
default: tumorID
reference: reference
out:
- mutations
fpfilterSomaticSniper:
run: ./tools/fpfilter-tool/fpfilter.cwl
in:
vcf-file: rawSomsniper
bam-file: tumor
reference: reference
output:
default: somatic_sniper_fpfilter.vcf
out:
- filtered_vcf
fpfilterVarscans:
run: ./tools/fpfilter-tool/fpfilter.cwl
in:
vcf-file: rawVarscans
bam-file: tumor
reference: reference
output:
default: varscan_fpfilter.vcf
out:
- filtered_vcf
filterMuse:
run: ./tools/muse-tool/muse.filter.cwl
in:
vcf: rawMuse
output_name:
default: muse_filtered.vcf
out:
- output_vcf
filterPindel:
run: ./tools/vcf-tools/filter_vcf.cwl
in:
vcf: rawPindel
output_name:
default: pindel_filtered.vcf
cutoff:
default: 3
out:
- output_vcf
filterIndelocator:
run: tools/vcf-tools/filter_vcf.cwl
in:
vcf: rawIndelocator
output_name:
default: indelocator_filtered.vcf
cutoff:
default: 3
tumorID: tumorID
normalID: normalID
out:
- output_vcf
outputs:
filteredRadiaVCF:
type: File
outputSource:
filterRadia/mutations
fpfilteredSomaticsniperVCF:
type: File
outputSource:
fpfilterSomaticSniper/filtered_vcf
fpfilteredVarscansVCF:
type: File
outputSource:
fpfilterVarscans/filtered_vcf
filteredMuseVCF:
type: File
outputSource:
filterMuse/output_vcf
filteredPindelVCF:
type: File
outputSource:
filterPindel/output_vcf
filteredIndelocatorVCF:
type: File
outputSource:
filterIndelocator/output_vcf