Newer
Older
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
params {
refSource = "biohpc"
}
process {
executor = 'slurm'
queue = 'super'
clusterOptions = '--hold'
time = '4h'
errorStrategy = 'retry'
maxRetries = 1
withName:trackStart {
executor = 'local'
}
withName:getBag {
executor = 'local'
}
withName:getData {
queue = 'super'
}
withName:parseMetadata {
executor = 'local'
}
withName:trimData {
queue = 'super'
}
withName:getRefInfer {
queue = 'super'
}
withName:downsampleData {
executor = 'local'
}
withName:alignSampleData {
queue = '128GB,256GB,256GBv1,384GB'
}
withName:inferMetadata {
queue = 'super'
}
withName:checkMetadata {
executor = 'local'
}
withName:getRef {
queue = 'super'
}
withName:alignData {
queue = '256GB,256GBv1'
}
withName:dedupData {
queue = 'super'
}
withName:countData {
queue = 'super'
}
withName:makeBigWig {
queue = 'super'
}
withName:fastqc {
queue = 'super'
}
withName:dataQC {
queue = 'super'
}
withName:aggrQC {
executor = 'local'
}
withName:uploadInputBag {
executor = 'local'
}
withName:uploadExecutionRun {
executor = 'local'
}
withName:uploadQC {
executor = 'local'
}
withName:uploadProcessedFile {
executor = 'local'
}
withName:uploadOutputBag {
executor = 'local'
}
withName:finalizeExecutionRun {
executor = 'local'
}
withName:failPreExecutionRun {
executor = 'local'
}
withName:failExecutionRun {
executor = 'local'
}
withName:uploadQC_fail {
executor = 'local'
}
}
singularity {
enabled = true
cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
}
env {
http_proxy = 'http://proxy.swmed.edu:3128'
https_proxy = 'http://proxy.swmed.edu:3128'
all_proxy = 'http://proxy.swmed.edu:3128'
}