Skip to content

Commit 38bf092

Browse files
julienlagjulienlag
committed
reformat json files. fix TOC in documentation.md
1 parent 5059211 commit 38bf092

6 files changed

+370
-371
lines changed

‎cluster_config.json

+197-197
Original file line numberDiff line numberDiff line change
@@ -1,198 +1,198 @@
11
{
2-
"__default__": {
3-
"queue": "rg-el7,short-sl7,long-sl7",
4-
"virtual_free": "5G",
5-
"h_rt": "03:00:00",
6-
"email": "julien.lagarde@crg.eu",
7-
"notify": "ae",
8-
"err": "{workflow.basedir}/qsub_logs/",
9-
"out": "{workflow.basedir}/qsub_logs/",
10-
"project": "prj006070",
11-
"threads": "",
12-
"disk": "2G"
13-
},
14-
"makeStarIndex": {
15-
"virtual_free": "40G",
16-
"h_rt": "06:00:00"
17-
},
18-
"strandedGffToBed": {
19-
"virtual_free": "15G"
20-
},
21-
"makeReadsBlastDB": {
22-
"h_rt": "00:20:00",
23-
"virtual_free": "2G"
24-
},
25-
"getHiSeqSupportedHCGMs": {
26-
"virtual_free": "15G"
27-
},
28-
"getReadLengthSummary": {
29-
"virtual_free": "20G",
30-
"h_rt": "01:30:00"
31-
},
32-
"makeBigWigExonicRegions": {
33-
"h_rt": "06:00:00"
34-
},
35-
"mergedUnfilteredSirvReads": {
36-
"h_rt": "05:30:00"
37-
},
38-
"plotReadLength": {
39-
"virtual_free": "25G",
40-
"h_rt": "01:30:00"
41-
},
42-
"aggTmStats": {
43-
"h_rt": "04:00:00"
44-
},
45-
"compareTargetsToTms": {
46-
"disk": "30G",
47-
"virtual_free": "15G"
48-
},
49-
"removeIntraPriming": {
50-
"virtual_free": "25G"
51-
},
52-
"getGeneReadCoverageStats": {
53-
"virtual_free": "25G",
54-
"h_rt": "20:00:00"
55-
},
56-
"longReadMapping": {
57-
"virtual_free": "40G",
58-
"h_rt": "20:00:00",
59-
"threads": "-pe smp 12",
60-
"queue": "rg-el7,long-sl7"
61-
},
62-
"hiSeqReadMapping": {
63-
"virtual_free": "70G",
64-
"h_rt": "20:00:00",
65-
"queue": "rg-el7,long-sl7",
66-
"threads": "-pe smp 12"
67-
},
68-
"highConfidenceReads": {
69-
"h_rt": "6:00:00",
70-
"virtual_free": "35G"
71-
},
72-
"readBedToGff": {
73-
"queue": "rg-el7,long-sl7",
74-
"h_rt": "10:00:00",
75-
"virtual_free": "5G"
76-
},
77-
"polyAmapping": {
78-
"h_rt": "3:00:00",
79-
"virtual_free": "2G"
80-
},
81-
"getPolyAreadsList": {
82-
"virtual_free": "1G"
83-
},
84-
"getPolyAreadsStats": {
85-
"h_rt": "6:00:00"
86-
},
87-
"makeIntrons": {
88-
"h_rt": "10:00:00",
89-
"queue": "rg-el7,long-sl7",
90-
"virtual_free": "20G"
91-
},
92-
"getIntronMotif": {
93-
"virtual_free": "15G"
94-
},
95-
"getReadsSpliceSites": {
96-
"virtual_free": "10G"
97-
},
98-
"getHiSSStats": {
99-
"virtual_free": "65G",
100-
"h_rt": "06:00:00"
101-
},
102-
"mergeWithRef": {
103-
"virtual_free": "20G",
104-
"h_rt": "06:00:00"
105-
},
106-
"mergedReads": {
107-
"virtual_free": "60G",
108-
"h_rt": "26:00:00"
109-
},
110-
"mergedReadsToBed": {
111-
"virtual_free": "10G"
112-
},
113-
"collapseGencode": {
114-
"virtual_free": "10G"
115-
},
116-
"getHiSeqCanonicalIntronsList1": {
117-
"h_rt": "6:00:00"
118-
},
119-
"getHiSeqCanonicalIntronsList2": {
120-
"virtual_free": "60G",
121-
"h_rt": "16:00:00",
122-
"threads": "-pe smp 6"
123-
},
124-
"plotHistTmLengthStats": {
125-
"virtual_free": "20G"
126-
},
127-
"gffcompareToAnnotation": {
128-
"virtual_free": "10G"
129-
},
130-
"gffcompareToSirvAnnotation": {
131-
"virtual_free": "1G"
132-
},
133-
"getHCGMintrons": {
134-
"virtual_free": "10G"
135-
},
136-
"getClsSpliceJunctions": {
137-
"h_rt": "04:30:00",
138-
"virtual_free": "10G"
139-
},
140-
"getTmSpliceSites": {
141-
"h_rt": "04:30:00"
142-
},
143-
"getCompareClsGencodeSJsStats": {
144-
"h_rt": "04:30:00"
145-
},
146-
"getGffCompareStats": {
147-
"h_rt": "04:30:00"
148-
},
149-
"cageSupportedfivepEnds": {
150-
"virtual_free": "15G"
151-
},
152-
"getReadBiotypeClassification": {
153-
"disk": "30G",
154-
"h_rt": "16:00:00"
155-
},
156-
"aggGeneidScores": {
157-
"threads": "-pe smp 8"
158-
},
159-
"plotGeneidScores": {
160-
"virtual_free": "35G",
161-
"h_rt": "5:30:00"
162-
},
163-
"getHiSeqMappingStats": {
164-
"h_rt": "8:00:00",
165-
"queue": "rg-el7,long-sl7"
166-
},
167-
"mergeTmsWithGencode": {
168-
"virtual_free": "10G",
169-
"h_rt": "5:00:00"
170-
},
171-
"polyASupportedthreepEnds": {
172-
"virtual_free": "15G"
173-
},
174-
"readBamToBed": {
175-
"virtual_free": "1G"
176-
},
177-
"tmergeAll": {
178-
"disk": "60G",
179-
"h_rt": "12:00:00",
180-
"virtual_free": "20G",
181-
"queue": "rg-el7,long-sl7"
182-
},
183-
"getReadProfileMatrix": {
184-
"h_rt": "12:00:00",
185-
"threads": "-pe smp 6",
186-
"queue": "rg-el7,long-sl7",
187-
"virtual_free": "15G"
188-
},
189-
"plotReadProfileMatrix": {
190-
"virtual_free": "20G"
191-
},
192-
"bamqc": {
193-
"virtual_free": "25G"
194-
},
195-
"mergedReadsGroupedSampleReps": {
196-
"virtual_free": "15G"
197-
}
198-
}
2+
"__default__": {
3+
"queue": "rg-el7,short-sl7,long-sl7",
4+
"virtual_free": "5G",
5+
"h_rt": "03:00:00",
6+
"email": "julien.lagarde@crg.eu",
7+
"notify": "ae",
8+
"err": "{workflow.basedir}/qsub_logs/",
9+
"out": "{workflow.basedir}/qsub_logs/",
10+
"project": "prj006070",
11+
"threads": "",
12+
"disk": "2G"
13+
},
14+
"makeStarIndex": {
15+
"virtual_free": "40G",
16+
"h_rt": "06:00:00"
17+
},
18+
"strandedGffToBed": {
19+
"virtual_free": "15G"
20+
},
21+
"makeReadsBlastDB": {
22+
"h_rt": "00:20:00",
23+
"virtual_free": "2G"
24+
},
25+
"getHiSeqSupportedHCGMs": {
26+
"virtual_free": "15G"
27+
},
28+
"getReadLengthSummary": {
29+
"virtual_free": "20G",
30+
"h_rt": "01:30:00"
31+
},
32+
"makeBigWigExonicRegions": {
33+
"h_rt": "06:00:00"
34+
},
35+
"mergedUnfilteredSirvReads": {
36+
"h_rt": "05:30:00"
37+
},
38+
"plotReadLength": {
39+
"virtual_free": "25G",
40+
"h_rt": "01:30:00"
41+
},
42+
"aggTmStats": {
43+
"h_rt": "04:00:00"
44+
},
45+
"compareTargetsToTms": {
46+
"disk": "30G",
47+
"virtual_free": "15G"
48+
},
49+
"removeIntraPriming": {
50+
"virtual_free": "25G"
51+
},
52+
"getGeneReadCoverageStats": {
53+
"virtual_free": "25G",
54+
"h_rt": "20:00:00"
55+
},
56+
"longReadMapping": {
57+
"virtual_free": "40G",
58+
"h_rt": "20:00:00",
59+
"threads": "-pe smp 12",
60+
"queue": "rg-el7,long-sl7"
61+
},
62+
"hiSeqReadMapping": {
63+
"virtual_free": "70G",
64+
"h_rt": "20:00:00",
65+
"queue": "rg-el7,long-sl7",
66+
"threads": "-pe smp 12"
67+
},
68+
"highConfidenceReads": {
69+
"h_rt": "6:00:00",
70+
"virtual_free": "35G"
71+
},
72+
"readBedToGff": {
73+
"queue": "rg-el7,long-sl7",
74+
"h_rt": "10:00:00",
75+
"virtual_free": "5G"
76+
},
77+
"polyAmapping": {
78+
"h_rt": "3:00:00",
79+
"virtual_free": "2G"
80+
},
81+
"getPolyAreadsList": {
82+
"virtual_free": "1G"
83+
},
84+
"getPolyAreadsStats": {
85+
"h_rt": "6:00:00"
86+
},
87+
"makeIntrons": {
88+
"h_rt": "10:00:00",
89+
"queue": "rg-el7,long-sl7",
90+
"virtual_free": "20G"
91+
},
92+
"getIntronMotif": {
93+
"virtual_free": "15G"
94+
},
95+
"getReadsSpliceSites": {
96+
"virtual_free": "10G"
97+
},
98+
"getHiSSStats": {
99+
"virtual_free": "65G",
100+
"h_rt": "06:00:00"
101+
},
102+
"mergeWithRef": {
103+
"virtual_free": "20G",
104+
"h_rt": "06:00:00"
105+
},
106+
"mergedReads": {
107+
"virtual_free": "60G",
108+
"h_rt": "26:00:00"
109+
},
110+
"mergedReadsToBed": {
111+
"virtual_free": "10G"
112+
},
113+
"collapseGencode": {
114+
"virtual_free": "10G"
115+
},
116+
"getHiSeqCanonicalIntronsList1": {
117+
"h_rt": "6:00:00"
118+
},
119+
"getHiSeqCanonicalIntronsList2": {
120+
"virtual_free": "60G",
121+
"h_rt": "16:00:00",
122+
"threads": "-pe smp 6"
123+
},
124+
"plotHistTmLengthStats": {
125+
"virtual_free": "20G"
126+
},
127+
"gffcompareToAnnotation": {
128+
"virtual_free": "10G"
129+
},
130+
"gffcompareToSirvAnnotation": {
131+
"virtual_free": "1G"
132+
},
133+
"getHCGMintrons": {
134+
"virtual_free": "10G"
135+
},
136+
"getClsSpliceJunctions": {
137+
"h_rt": "04:30:00",
138+
"virtual_free": "10G"
139+
},
140+
"getTmSpliceSites": {
141+
"h_rt": "04:30:00"
142+
},
143+
"getCompareClsGencodeSJsStats": {
144+
"h_rt": "04:30:00"
145+
},
146+
"getGffCompareStats": {
147+
"h_rt": "04:30:00"
148+
},
149+
"cageSupportedfivepEnds": {
150+
"virtual_free": "15G"
151+
},
152+
"getReadBiotypeClassification": {
153+
"disk": "30G",
154+
"h_rt": "16:00:00"
155+
},
156+
"aggGeneidScores": {
157+
"threads": "-pe smp 8"
158+
},
159+
"plotGeneidScores": {
160+
"virtual_free": "35G",
161+
"h_rt": "5:30:00"
162+
},
163+
"getHiSeqMappingStats": {
164+
"h_rt": "8:00:00",
165+
"queue": "rg-el7,long-sl7"
166+
},
167+
"mergeTmsWithGencode": {
168+
"virtual_free": "10G",
169+
"h_rt": "5:00:00"
170+
},
171+
"polyASupportedthreepEnds": {
172+
"virtual_free": "15G"
173+
},
174+
"readBamToBed": {
175+
"virtual_free": "1G"
176+
},
177+
"tmergeAll": {
178+
"disk": "60G",
179+
"h_rt": "12:00:00",
180+
"virtual_free": "20G",
181+
"queue": "rg-el7,long-sl7"
182+
},
183+
"getReadProfileMatrix": {
184+
"h_rt": "12:00:00",
185+
"threads": "-pe smp 6",
186+
"queue": "rg-el7,long-sl7",
187+
"virtual_free": "15G"
188+
},
189+
"plotReadProfileMatrix": {
190+
"virtual_free": "20G"
191+
},
192+
"bamqc": {
193+
"virtual_free": "25G"
194+
},
195+
"mergedReadsGroupedSampleReps": {
196+
"virtual_free": "15G"
197+
}
198+
}

0 commit comments

Comments
 (0)