cluster_config.json

{
	"__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": "40G"
	},
	"strandGffs": {
		"virtual_free": "10G",
		"h_rt": "15:00:00"
	},
	"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": "36:00:00",
		"virtual_free": "50G"
	},
	"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": "25G"
	},
	"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": "120G",
		"h_rt": "36:00:00"
	},
	"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"
	},
	"catMergedReadsForGroupedSampleReps": {
		"virtual_free": "20G"
	},
	"gffcompareToAnnotation": {
		"virtual_free": "10G"
	},
	"gffcompareToSirvAnnotation": {
		"virtual_free": "1G"
	},
	"getHCGMintrons": {
		"virtual_free": "20G"
	},
	"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": "30:00:00"
	},
	"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"
	}
}