-
Notifications
You must be signed in to change notification settings - Fork 5
/
EXAMPLE_cluster_singularity_slurm_bigwig.json
193 lines (176 loc) · 6.38 KB
/
EXAMPLE_cluster_singularity_slurm_bigwig.json
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
{
"__default__":
{
"project-name":"b097",
"job-name" : "{rule}",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "2:30:00",
"memory" : "5G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.replicat_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.replicat_name}_slurm.err",
"mail-type":"BEGIN,END",
"mail-user":"hammal_10@hotmail.fr"
},
"aria2":
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "12:00:00",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.fastq_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.fastq_name}_slurm.err"
},
"trim_galore" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "9:00:00"
},
"bowtie2" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "16",
"ntasks" : "1",
"time" : "7:00:00"
},
"delete_trim_paired" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "0:05:00",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.replicat_name_paired}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.replicat_name_paired}_slurm.err"
},
"samtools_remove_unmapped" :
{
"job-name" : "RMunmapped",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "5:30:00"
},
"remove_mismatch" :
{
"job-name" : "RMmismatch",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"time" : "5:00:00"
},
"samtools_sort" :
{
"job-name" : "sort",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"time" : "4:20:00"
},
"samtools_remove_pcr_duplicate" :
{
"job-name" : "RMpcrdup",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "5:00:00"
},
"macs2_bigwig" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"removing_weird_chromosome" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"sort_bedgraph" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"clipping_bedgraph" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"bedgraph_to_bigwig" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"merge_bam" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
},
"quality_FRiP" :
{
"queue" : "remap",
"node" : "1",
"thread" : "1",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
},
"quality_NSC_RSC" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "2",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
},
"quality_all" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
}
}