-
Notifications
You must be signed in to change notification settings - Fork 1
/
pindel.cwl
206 lines (169 loc) · 3.45 KB
/
pindel.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
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
class: CommandLineTool
label: Pindel-Somatic
cwlVersion: v1.0
baseCommand: ["python", "/opt/pindel.py", "-t", "NORMAL", "-t", "TUMOR"]
requirements:
- class: DockerRequirement
dockerPull: opengenomics/pindel:latest
inputs:
- id: normal
type: File
inputBinding:
position: 1
prefix: -b
- id: tumor
type: File
inputBinding:
position: 2
prefix: -b
- id: normal_insert_size
type: int?
inputBinding:
position: 1
prefix: -s
- id: tumor_insert_size
type: int?
inputBinding:
position: 2
prefix: -s
- id: reference
type: File
inputBinding:
prefix: -r
- id: centromere
type: File
inputBinding:
prefix: -J
- id: referenceName
type: string
default: HG19
inputBinding:
prefix: -R
- id: window_size
type: float
default: 5.0
inputBinding:
prefix: --window_size
- id: balance_cutoff
type: int
default: 100
inputBinding:
prefix: --balance_cutoff
- id: procs
type: int
default: 2
inputBinding:
prefix: --number_of_procs
- id: report_inversions
type: boolean
default: false
inputBinding:
prefix: --report_inversions
- id: report_duplications
type: boolean
default: false
inputBinding:
prefix: --report_duplications
- id: report_long_insertions
type: boolean
default: false
inputBinding:
prefix: --report_long_insertions
- id: report_breakpoints
type: boolean
default: false
inputBinding:
prefix: --report_breakpoints
- id: report_only_close_mapped_reads
type: boolean
default: false
inputBinding:
prefix: -S
- id: outputRawFile
type: string
default: pindel.raw
inputBinding:
prefix: -o1
- id: outputVcfFile
type: string
default: pindel.vcf
inputBinding:
prefix: -o2
- id: outputSomaticVcfFile
type: string
default: pindel_somatic.vcf
inputBinding:
prefix: -o3
- id: somatic_vaf
type: float
default: 0.08
inputBinding:
prefix: --somatic_vaf
- id: somatic_cov
type: int
default: 20
inputBinding:
prefix: --somatic_cov
- id: somatic_hom
type: int
default: 6
inputBinding:
prefix: --somatic_hom
- id: min_inversion_size
type: int
default: 50
inputBinding:
prefix: --min_inversion_size
- id: min_num_matched_bases
type: int
default: 30
inputBinding:
prefix: -d
- id: max_range_index
type: int
default: 4
inputBinding:
prefix: -x
- id: additional_mismatch
type: int
default: 1
inputBinding:
prefix: -a
- id: min_perfect_match_around_BP
type: int
default: 3
inputBinding:
prefix: -m
- id: sequencing_error_rate
type: float
default: 0.01
inputBinding:
prefix: --sequencing_error_rate
- id: maximum_allowed_mismatch_rate
type: float
default: 0.02
inputBinding:
prefix: --maximum_allowed_mismatch_rate
- id: minimum_support_for_event
type: int
default: 1
inputBinding:
prefix: -M
- id: sensitivity
type: float
default: 0.95
inputBinding:
prefix: --sensitivity
outputs:
- id: vcf
type: File
outputBinding:
glob: pindel.vcf
- id: somatic_vcf
type: File
outputBinding:
glob: pindel_somatic.vcf
- id: rawFile
type: File
outputBinding:
glob: pindel.raw