-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsomatic_mutation_analysis
146 lines (142 loc) · 3.26 KB
/
somatic_mutation_analysis
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
class: Workflow
cwlVersion: v1.1
label: somatic_mutation_analysis
$namespaces:
sbg: https://sevenbridges.com
requirements:
- class: ScatterFeatureRequirement
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
inputs:
- id: maf
type: File[]?
sbg:x: -70
sbg:y: 205
outputs:
- id: oncoplots
type: File?
outputSource:
- oncoplot/oncoplot
sbg:x: 574.1786499023438
sbg:y: 472
- id: summary_plot
type: File?
outputSource:
- maftools_read_and_summary/summary_plot
sbg:x: 318.9014892578125
sbg:y: 86
- id: signatures_plot
type: File?
outputSource:
- somatic_signatures/signatures_plot
sbg:x: 619.1786499023438
sbg:y: 0
- id: signature_heatmap
type: File?
outputSource:
- somatic_signatures/signature_heatmap
sbg:x: 619.1786499023438
sbg:y: 107
- id: cophenetic_plot
type: File?
outputSource:
- somatic_signatures/cophenetic_plot
sbg:x: 629.1786499023438
sbg:y: 240
- id: APOBEC
type: File?
outputSource:
- somatic_signatures/APOBEC
sbg:x: 633.1786499023438
sbg:y: 355
steps:
- id: oncoplot
label: oncoplot
in:
- id: maf_object
source: maftools_read_and_summary/maf_object
scatter:
- maf_object
run: somatic_mutation_analysis.steps/oncoplot.cwl
out:
- id: oncoplot
sbg:x: 318.9014892578125
sbg:y: 342
- id: maftools_read_and_summary
label: maftools_read_and_summary
in:
- id: maf
source: maf
scatter:
- maf
run: somatic_mutation_analysis.steps/maftools_read_and_summary.cwl
out:
- id: summary_plot
- id: maf_object
sbg:x: 105
sbg:y: 207
- id: somatic_signatures
label: somatic_signatures
in:
- id: maf_object
source: maftools_read_and_summary/maf_object
scatter:
- maf_object
run: somatic_mutation_analysis.steps/somatic_signatures.cwl
out:
- id: APOBEC
- id: cophenetic_plot
- id: signature_heatmap
- id: signatures_plot
sbg:x: 318.9014892578125
sbg:y: 214
sbg:appVersion:
- v1.1
sbg:content_hash: a4ccf4aed2e6e1945e9839f6783e651d34dda2bf34ac969098081d6e370d79e49
sbg:contributors:
- david.roberson
sbg:createdBy: david.roberson
sbg:createdOn: 1611589223
sbg:id: david.roberson/maftools-demo/somatic-mutation-analysis/6
sbg:image_url:
sbg:latestRevision: 6
sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611595780
sbg:original_source: |-
https://cgc-api.sbgenomics.com/v2/apps/david.roberson/maftools-demo/somatic-mutation-analysis/6/raw/
sbg:project: david.roberson/maftools-demo
sbg:projectName: maftools demo
sbg:publisher: sbg
sbg:revision: 6
sbg:revisionNotes: ''
sbg:revisionsInfo:
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611589223
sbg:revision: 0
sbg:revisionNotes:
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611589281
sbg:revision: 1
sbg:revisionNotes: ''
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611593140
sbg:revision: 2
sbg:revisionNotes: ''
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611594690
sbg:revision: 3
sbg:revisionNotes: ''
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611595018
sbg:revision: 4
sbg:revisionNotes: ''
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611595386
sbg:revision: 5
sbg:revisionNotes: ''
- sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1611595780
sbg:revision: 6
sbg:revisionNotes: ''
sbg:sbgMaintained: false
sbg:validationErrors: []