-
Notifications
You must be signed in to change notification settings - Fork 2
/
.dockstore.yml
141 lines (141 loc) · 5.61 KB
/
.dockstore.yml
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
version: 1.2
workflows:
- name: SmartSeq2_scRNA_pipeline
subclass: WDL
primaryDescriptorPath: /SmartSeq/scRNA_Pipeline/SmartSeq2_scRNA_pipeline.wdl
testParameterFiles:
- /SmartSeq/scRNA_Pipeline/SmartSeq2_scRNA_pipeline.human.terra-inputs.json
- /SmartSeq/scRNA_Pipeline/SmartSeq2_scRNA_pipeline.mouse.terra-inputs.json
- name: SmartSeq2_SC_Plate_QC
subclass: WDL
primaryDescriptorPath: /SmartSeq/SC_Plate_QC/SC_Plate_QC.wdl
testParameterFiles:
- /SmartSeq/SC_Plate_QC/SC_Plate_QC.human.terra-inputs.json
- /SmartSeq/SC_Plate_QC/SC_Plate_QC.mouse.terra-inputs.json
- name: CollectSamErrorMetrics
subclass: WDL
primaryDescriptorPath: /CollectSamError/CollectSamErrorMetrics.wdl
testParameterFiles:
- /CollectSamError/CollectSamErrorMetrics.inputs.json
- name: GATK4_CNV
subclass: WDL
primaryDescriptorPath: /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.wdl
testParameterFiles:
- /GATK_CNV_Mutect2/GATK4_CNV/GATK4_CNVSomaticPairWorkflow.inputs.json
- name: mutect2-gatk4
subclass: WDL
primaryDescriptorPath: /GATK_CNV_Mutect2/mutect2-gatk4/mutect2-gatk4.wdl
testParameterFiles:
- /Users/gaoyueya/Documents/GitHub/TAG-public/GATK_CNV_Mutect2/mutect2-gatk4/mutect2-gatk4.inputs.json
- name: GenerateDuplexConsensusBams
subclass: WDL
primaryDescriptorPath: /Liquid_Biopsy_Duplex_Analysis/GenerateDuplexConsensusBams/GenerateDuplexConsensusBams.wdl
testParameterFiles:
- /Liquid_Biopsy_Duplex_Analysis/GenerateDuplexConsensusBams/GenerateDuplexConsensusBams.inputs.json
- name: MakeCallsFromConsensus
subclass: WDL
primaryDescriptorPath: /Liquid_Biopsy_Duplex_Analysis/MakeCallsFromConsensus/MakeCallsFromConsensus.wdl
testParameterFiles:
- /Liquid_Biopsy_Duplex_Analysis/MakeCallsFromConsensus/MakeCallsFromConsensus.T-N.inputs.json
- /Liquid_Biopsy_Duplex_Analysis/MakeCallsFromConsensus/MakeCallsFromConsensus.T-only.inputs.json
- name: iChorCNA_hg19
subclass: WDL
primaryDescriptorPath: /iChor/iChorCNA_hg19/iChorCNA_hg19.wdl
testParameterFiles:
- /iChor/iChorCNA_hg19/iChorCNA_hg19.inputs.json
- name: iChorCNA_hg38
subclass: WDL
primaryDescriptorPath: /iChor/iChorCNA_hg38/iChorCNA_hg38.wdl
testParameterFiles:
- /iChor/iChorCNA_hg38/iChorCNA_hg38.inputs.json
- name: iChorCNA_step2
subclass: WDL
primaryDescriptorPath: /iChor/iChorCNA_step2/iChorCNA_step2.wdl
testParameterFiles:
- /iChor/iChorCNA_step2/iChorCNA_step2.inputs.json
- name: lego_plotter
subclass: WDL
primaryDescriptorPath: /LegoPlotter/lego_plotter.wdl
testParameterFiles:
- /LegoPlotter/lego_plotter.inputs.json
- name: SomaticSV_SvABA
subclass: WDL
primaryDescriptorPath: /SomaticSV_SvABA/SomaticSV_SvABA.wdl
testParameterFiles:
- /SomaticSV_SvABA/SomaticSV_SvABA.inputs.json
- /SomaticSV_SvABA/SomaticSV_SvABA_Tonly.inputs.json
- name: BreaKmer
subclass: WDL
primaryDescriptorPath: /BreaKmer/BreaKmer.wdl
testParameterFiles:
- /BreaKmer/BreaKmer.inputs.json
- name: Griffin_GC_Correction
subclass: WDL
primaryDescriptorPath: /Griffin/griffin_GC_correction/griffin_GC_correction.wdl
testParameterFiles:
- /Griffin/griffin_GC_correction/griffin_GC_correction.inputs.json
- name: Griffin_Nucleosome_Profiling
subclass: WDL
primaryDescriptorPath: /Griffin/griffin_nucleosome_profiling/griffin_nucleosome_profiling.wdl
testParameterFiles:
- /Griffin/griffin_nucleosome_profiling/griffin_nucleosome_profiling.inputs.json
- name: griffin_ER_classifier
subclass: WDL
primaryDescriptorPath: /Griffin/griffin_ER_classifier/griffin_ER_classifier.wdl
testParameterFiles:
- /Griffin/griffin_ER_classifier/griffin_ER_classifier.inputs.json
- name: checkBaitSetName
subclass: WDL
primaryDescriptorPath: /checkBaitSetName/checkBaitSetName.wdl
testParameterFiles:
- /checkBaitSetName/checkBaitSetName.inputs.json
- name: SelectSampleFromCallSet
subclass: WDL
primaryDescriptorPath: /BenchmarkCNV/SelectSampleFromCallSet/SelectSampleFromCallSet.wdl
testParameterFiles:
- /BenchmarkCNV/SelectSampleFromCallSet/SelectSampleFromCallSet.inputs.json
- name: MergeVCF
subclass: WDL
primaryDescriptorPath: /BenchmarkCNV/MergeVCF/MergeVCF.wdl
testParameterFiles:
- /BenchmarkCNV/MergeVCF/MergeVCF.inputs.json
- name: BenchmarkCNV
subclass: WDL
primaryDescriptorPath: /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.wdl
testParameterFiles:
- /BenchmarkCNV/BenchmarkCNV/BenchmarkCNV.inputs.json
- name: checkBaitSetName_dev
subclass: WDL
primaryDescriptorPath: /checkBaitSetName/checkBaitSetName.dev.wdl
testParameterFiles:
- /checkBaitSetName/checkBaitSetName.dev.inputs.json
- name: DownsampleBam
subclass: WDL
primaryDescriptorPath: /DownsampleBam/DownsampleBam.wdl
testParameterFiles:
- /DownsampleBam/DownsampleBam.inputs.json
- name: Cleanup_Failed_Submissions
subclass: WDL
primaryDescriptorPath: /CleanupFailedSubmissions/Cleanup_Failed_Submissions.wdl
testParameterFiles:
- /CleanupFailedSubmissions/Cleanup_Failed_Submissions.inputs.json
- name: TAG_Mop
subclass: WDL
primaryDescriptorPath: /TAG_Mop/TAG_Mop.wdl
testParameterFiles:
- /TAG_Mop/TAG_Mop.inputs.json
- name: QUICviz
subclass: WDL
primaryDescriptorPath: /PECGS-QUICviz/QUICviz.wdl
testParameterFiles:
- /PECGS-QUICviz/QUICviz.inputs.json
- name: PeddyAnalysis
subclass: WDL
primaryDescriptorPath: /PeddyAnalysis/PeddyAnalysis.wdl
testParameterFiles:
- /PeddyAnalysis/PeddyAnalysis.inputs.json
- name: cnvArrayProber
subclass: WDL
primaryDescriptorPath: /CNV_Array_Prober/cnvArrayProber.wdl
testParameterFiles:
- /CNV_Array_Prober/cnvArrayProber.inputs.json