-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
reformat json files. fix TOC in documentation.md
- Loading branch information
Showing
6 changed files
with
370 additions
and
371 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,198 +1,198 @@ | ||
| { | ||
| "__default__": { | ||
| "queue": "rg-el7,short-sl7,long-sl7", | ||
| "virtual_free": "5G", | ||
| "h_rt": "03:00:00", | ||
| "email": "julien.lagarde@crg.eu", | ||
| "notify": "ae", | ||
| "err": "{workflow.basedir}/qsub_logs/", | ||
| "out": "{workflow.basedir}/qsub_logs/", | ||
| "project": "prj006070", | ||
| "threads": "", | ||
| "disk": "2G" | ||
| }, | ||
| "makeStarIndex": { | ||
| "virtual_free": "40G", | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "strandedGffToBed": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "makeReadsBlastDB": { | ||
| "h_rt": "00:20:00", | ||
| "virtual_free": "2G" | ||
| }, | ||
| "getHiSeqSupportedHCGMs": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "getReadLengthSummary": { | ||
| "virtual_free": "20G", | ||
| "h_rt": "01:30:00" | ||
| }, | ||
| "makeBigWigExonicRegions": { | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "mergedUnfilteredSirvReads": { | ||
| "h_rt": "05:30:00" | ||
| }, | ||
| "plotReadLength": { | ||
| "virtual_free": "25G", | ||
| "h_rt": "01:30:00" | ||
| }, | ||
| "aggTmStats": { | ||
| "h_rt": "04:00:00" | ||
| }, | ||
| "compareTargetsToTms": { | ||
| "disk": "30G", | ||
| "virtual_free": "15G" | ||
| }, | ||
| "removeIntraPriming": { | ||
| "virtual_free": "25G" | ||
| }, | ||
| "getGeneReadCoverageStats": { | ||
| "virtual_free": "25G", | ||
| "h_rt": "20:00:00" | ||
| }, | ||
| "longReadMapping": { | ||
| "virtual_free": "40G", | ||
| "h_rt": "20:00:00", | ||
| "threads": "-pe smp 12", | ||
| "queue": "rg-el7,long-sl7" | ||
| }, | ||
| "hiSeqReadMapping": { | ||
| "virtual_free": "70G", | ||
| "h_rt": "20:00:00", | ||
| "queue": "rg-el7,long-sl7", | ||
| "threads": "-pe smp 12" | ||
| }, | ||
| "highConfidenceReads": { | ||
| "h_rt": "6:00:00", | ||
| "virtual_free": "35G" | ||
| }, | ||
| "readBedToGff": { | ||
| "queue": "rg-el7,long-sl7", | ||
| "h_rt": "10:00:00", | ||
| "virtual_free": "5G" | ||
| }, | ||
| "polyAmapping": { | ||
| "h_rt": "3:00:00", | ||
| "virtual_free": "2G" | ||
| }, | ||
| "getPolyAreadsList": { | ||
| "virtual_free": "1G" | ||
| }, | ||
| "getPolyAreadsStats": { | ||
| "h_rt": "6:00:00" | ||
| }, | ||
| "makeIntrons": { | ||
| "h_rt": "10:00:00", | ||
| "queue": "rg-el7,long-sl7", | ||
| "virtual_free": "20G" | ||
| }, | ||
| "getIntronMotif": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "getReadsSpliceSites": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getHiSSStats": { | ||
| "virtual_free": "65G", | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "mergeWithRef": { | ||
| "virtual_free": "20G", | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "mergedReads": { | ||
| "virtual_free": "60G", | ||
| "h_rt": "26:00:00" | ||
| }, | ||
| "mergedReadsToBed": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "collapseGencode": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getHiSeqCanonicalIntronsList1": { | ||
| "h_rt": "6:00:00" | ||
| }, | ||
| "getHiSeqCanonicalIntronsList2": { | ||
| "virtual_free": "60G", | ||
| "h_rt": "16:00:00", | ||
| "threads": "-pe smp 6" | ||
| }, | ||
| "plotHistTmLengthStats": { | ||
| "virtual_free": "20G" | ||
| }, | ||
| "gffcompareToAnnotation": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "gffcompareToSirvAnnotation": { | ||
| "virtual_free": "1G" | ||
| }, | ||
| "getHCGMintrons": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getClsSpliceJunctions": { | ||
| "h_rt": "04:30:00", | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getTmSpliceSites": { | ||
| "h_rt": "04:30:00" | ||
| }, | ||
| "getCompareClsGencodeSJsStats": { | ||
| "h_rt": "04:30:00" | ||
| }, | ||
| "getGffCompareStats": { | ||
| "h_rt": "04:30:00" | ||
| }, | ||
| "cageSupportedfivepEnds": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "getReadBiotypeClassification": { | ||
| "disk": "30G", | ||
| "h_rt": "16:00:00" | ||
| }, | ||
| "aggGeneidScores": { | ||
| "threads": "-pe smp 8" | ||
| }, | ||
| "plotGeneidScores": { | ||
| "virtual_free": "35G", | ||
| "h_rt": "5:30:00" | ||
| }, | ||
| "getHiSeqMappingStats": { | ||
| "h_rt": "8:00:00", | ||
| "queue": "rg-el7,long-sl7" | ||
| }, | ||
| "mergeTmsWithGencode": { | ||
| "virtual_free": "10G", | ||
| "h_rt": "5:00:00" | ||
| }, | ||
| "polyASupportedthreepEnds": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "readBamToBed": { | ||
| "virtual_free": "1G" | ||
| }, | ||
| "tmergeAll": { | ||
| "disk": "60G", | ||
| "h_rt": "12:00:00", | ||
| "virtual_free": "20G", | ||
| "queue": "rg-el7,long-sl7" | ||
| }, | ||
| "getReadProfileMatrix": { | ||
| "h_rt": "12:00:00", | ||
| "threads": "-pe smp 6", | ||
| "queue": "rg-el7,long-sl7", | ||
| "virtual_free": "15G" | ||
| }, | ||
| "plotReadProfileMatrix": { | ||
| "virtual_free": "20G" | ||
| }, | ||
| "bamqc": { | ||
| "virtual_free": "25G" | ||
| }, | ||
| "mergedReadsGroupedSampleReps": { | ||
| "virtual_free": "15G" | ||
| } | ||
| } | ||
| "__default__": { | ||
| "queue": "rg-el7,short-sl7,long-sl7", | ||
| "virtual_free": "5G", | ||
| "h_rt": "03:00:00", | ||
| "email": "julien.lagarde@crg.eu", | ||
| "notify": "ae", | ||
| "err": "{workflow.basedir}/qsub_logs/", | ||
| "out": "{workflow.basedir}/qsub_logs/", | ||
| "project": "prj006070", | ||
| "threads": "", | ||
| "disk": "2G" | ||
| }, | ||
| "makeStarIndex": { | ||
| "virtual_free": "40G", | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "strandedGffToBed": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "makeReadsBlastDB": { | ||
| "h_rt": "00:20:00", | ||
| "virtual_free": "2G" | ||
| }, | ||
| "getHiSeqSupportedHCGMs": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "getReadLengthSummary": { | ||
| "virtual_free": "20G", | ||
| "h_rt": "01:30:00" | ||
| }, | ||
| "makeBigWigExonicRegions": { | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "mergedUnfilteredSirvReads": { | ||
| "h_rt": "05:30:00" | ||
| }, | ||
| "plotReadLength": { | ||
| "virtual_free": "25G", | ||
| "h_rt": "01:30:00" | ||
| }, | ||
| "aggTmStats": { | ||
| "h_rt": "04:00:00" | ||
| }, | ||
| "compareTargetsToTms": { | ||
| "disk": "30G", | ||
| "virtual_free": "15G" | ||
| }, | ||
| "removeIntraPriming": { | ||
| "virtual_free": "25G" | ||
| }, | ||
| "getGeneReadCoverageStats": { | ||
| "virtual_free": "25G", | ||
| "h_rt": "20:00:00" | ||
| }, | ||
| "longReadMapping": { | ||
| "virtual_free": "40G", | ||
| "h_rt": "20:00:00", | ||
| "threads": "-pe smp 12", | ||
| "queue": "rg-el7,long-sl7" | ||
| }, | ||
| "hiSeqReadMapping": { | ||
| "virtual_free": "70G", | ||
| "h_rt": "20:00:00", | ||
| "queue": "rg-el7,long-sl7", | ||
| "threads": "-pe smp 12" | ||
| }, | ||
| "highConfidenceReads": { | ||
| "h_rt": "6:00:00", | ||
| "virtual_free": "35G" | ||
| }, | ||
| "readBedToGff": { | ||
| "queue": "rg-el7,long-sl7", | ||
| "h_rt": "10:00:00", | ||
| "virtual_free": "5G" | ||
| }, | ||
| "polyAmapping": { | ||
| "h_rt": "3:00:00", | ||
| "virtual_free": "2G" | ||
| }, | ||
| "getPolyAreadsList": { | ||
| "virtual_free": "1G" | ||
| }, | ||
| "getPolyAreadsStats": { | ||
| "h_rt": "6:00:00" | ||
| }, | ||
| "makeIntrons": { | ||
| "h_rt": "10:00:00", | ||
| "queue": "rg-el7,long-sl7", | ||
| "virtual_free": "20G" | ||
| }, | ||
| "getIntronMotif": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "getReadsSpliceSites": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getHiSSStats": { | ||
| "virtual_free": "65G", | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "mergeWithRef": { | ||
| "virtual_free": "20G", | ||
| "h_rt": "06:00:00" | ||
| }, | ||
| "mergedReads": { | ||
| "virtual_free": "60G", | ||
| "h_rt": "26:00:00" | ||
| }, | ||
| "mergedReadsToBed": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "collapseGencode": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getHiSeqCanonicalIntronsList1": { | ||
| "h_rt": "6:00:00" | ||
| }, | ||
| "getHiSeqCanonicalIntronsList2": { | ||
| "virtual_free": "60G", | ||
| "h_rt": "16:00:00", | ||
| "threads": "-pe smp 6" | ||
| }, | ||
| "plotHistTmLengthStats": { | ||
| "virtual_free": "20G" | ||
| }, | ||
| "gffcompareToAnnotation": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "gffcompareToSirvAnnotation": { | ||
| "virtual_free": "1G" | ||
| }, | ||
| "getHCGMintrons": { | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getClsSpliceJunctions": { | ||
| "h_rt": "04:30:00", | ||
| "virtual_free": "10G" | ||
| }, | ||
| "getTmSpliceSites": { | ||
| "h_rt": "04:30:00" | ||
| }, | ||
| "getCompareClsGencodeSJsStats": { | ||
| "h_rt": "04:30:00" | ||
| }, | ||
| "getGffCompareStats": { | ||
| "h_rt": "04:30:00" | ||
| }, | ||
| "cageSupportedfivepEnds": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "getReadBiotypeClassification": { | ||
| "disk": "30G", | ||
| "h_rt": "16:00:00" | ||
| }, | ||
| "aggGeneidScores": { | ||
| "threads": "-pe smp 8" | ||
| }, | ||
| "plotGeneidScores": { | ||
| "virtual_free": "35G", | ||
| "h_rt": "5:30:00" | ||
| }, | ||
| "getHiSeqMappingStats": { | ||
| "h_rt": "8:00:00", | ||
| "queue": "rg-el7,long-sl7" | ||
| }, | ||
| "mergeTmsWithGencode": { | ||
| "virtual_free": "10G", | ||
| "h_rt": "5:00:00" | ||
| }, | ||
| "polyASupportedthreepEnds": { | ||
| "virtual_free": "15G" | ||
| }, | ||
| "readBamToBed": { | ||
| "virtual_free": "1G" | ||
| }, | ||
| "tmergeAll": { | ||
| "disk": "60G", | ||
| "h_rt": "12:00:00", | ||
| "virtual_free": "20G", | ||
| "queue": "rg-el7,long-sl7" | ||
| }, | ||
| "getReadProfileMatrix": { | ||
| "h_rt": "12:00:00", | ||
| "threads": "-pe smp 6", | ||
| "queue": "rg-el7,long-sl7", | ||
| "virtual_free": "15G" | ||
| }, | ||
| "plotReadProfileMatrix": { | ||
| "virtual_free": "20G" | ||
| }, | ||
| "bamqc": { | ||
| "virtual_free": "25G" | ||
| }, | ||
| "mergedReadsGroupedSampleReps": { | ||
| "virtual_free": "15G" | ||
| } | ||
| } |
Oops, something went wrong.