-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsge.yaml
167 lines (129 loc) · 2.85 KB
/
sge.yaml
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
__default__:
jobname: "{rule}"
parallelenvironment : 'smp 8'
logoutputdir : "$PWD/logs"
erroroutputdir : "$PWD/logs"
joinlogs : 'y'
memory: "h_vmem=8G"
generateTranscripts:
parallelenvironment : 'smp 10'
memory: "h_vmem=2G"
# auxillary.smk
processAnnotation:
parallelenvironment : 'smp 1'
memory: "h_vmem=4G"
generateMetageneRoi:
parallelenvironment : 'smp 1'
memory: "h_vmem=8G"
psiteOffsets:
parallelenvironment : 'smp 1'
memory: "h_vmem=8G"
gff2gtf:
parallelenvironment : 'smp 1'
memory: "h_vmem=4G"
# coverage.smk
coverage:
parallelenvironment : 'smp 1'
memory: "h_vmem=8G"
# deepribo.smk
parseDeepRibo:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
predictDeepRibo:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
# indexing
genomeSamToolsIndex:
parallelenvironment : 'smp 1'
memory: "h_vmem=8G"
genomeSize:
parallelenvironment : 'smp 1'
memory: "h_vmem=8G"
bamindex:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
# maplink.smk + tis
maplink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
ribomaplink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
ribobamindexlink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
rnamaplink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
rnabamindexlink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
tismaplink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
tisbamindexlink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
rnatismaplink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
rnatisbamindexlink:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
# mapping.smk
genomeSegemehlIndex:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
map:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
samuniq:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
samtobam:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
# preprocessing.smk
retrieveGenome:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
retrieveAnnotation:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
# reparation
reparation:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
uniprotDBRetrieve:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
# ribotish
ribotish:
parallelenvironment : 'smp 10'
memory: "h_vmem=2G"
ribotishQualityTIS:
parallelenvironment : 'smp 10'
memory: "h_vmem=2G"
ribotishQualityRIBO:
parallelenvironment : 'smp 10'
memory: "h_vmem=2G"
ribotishAnnotation:
parallelenvironment : 'smp 1'
memory: "h_vmem=4G"
# rrnafiltering.smk
rrnaretrieve:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
rrnaindex:
parallelenvironment : 'smp 1'
memory: "h_vmem=20G"
rrnafilter:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"
# trimming.smk
linktrim:
parallelenvironment : 'smp 1'
memory: "h_vmem=1G"
trim:
parallelenvironment : 'smp 20'
memory: "h_vmem=2G"