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Commit a1da775e authored by Christian Arnold's avatar Christian Arnold
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Changes to cluster.json

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......@@ -3,7 +3,7 @@
"queueSLURM": "htc",
"group": "zaugg",
"nCPUs": "{threads}",
"memory": 10000,
"memory": 20000,
"nodes": "avx2",
"maxTime": "5:00:00",
"qos": "normal",
......@@ -13,19 +13,19 @@
"willBeIgnored_canBeDeleted": "SEE ALSO BELOW IN THE RULES FOR MORE OCCURENCES OF OUTPUT AND ERROR FILES TO BE REPLACED"
},
"fastqc_BT": {
"memory": 5000,
"memory": 10000,
"maxTime": "2:00:00"
},
"trimming_PE": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"fastqc_AT": {
"memory": 5000,
"memory": 10000,
"maxTime": "2:00:00"
},
"Bowtie2_alignment": {
"memory": 15000,
"memory": 25000,
"maxTime": "24:00:00"
},
"samtools_SAM_TO_BAM": {
......@@ -33,15 +33,15 @@
"maxTime": "5:00:00"
},
"Picard_cleanSAM": {
"memory": 5000,
"memory": 20000,
"maxTime": "5:00:00"
},
"Picard_FixMateInformation": {
"memory": 15000,
"memory": 25000,
"maxTime": "5:00:00"
},
"Picard_AddOrReplaceReadGroups": {
"memory": 5000,
"memory": 10000,
"maxTime": "5:00:00"
},
"Picard_ReorderSam": {
......@@ -65,7 +65,7 @@
"maxTime": "10:00:00"
},
"postalign_remove_chrMAndUnassembledChr": {
"memory": 1000,
"memory": 10000,
"maxTime": "5:00:00"
},
"markDuplicates_Picardtools": {
......@@ -73,31 +73,31 @@
"maxTime": "10:00:00"
},
"computeLibraryComplexity": {
"memory": 1000,
"memory": 10000,
"maxTime": "2:00:00"
},
"removeDuplicates": {
"memory": 1000,
"memory": 10000,
"maxTime": "5:00:00"
},
"postalign_MAPQ": {
"memory": 1000,
"memory": 10000,
"maxTime": "5:00:00"
},
"postaling_RSS": {
"memory": 1000,
"memory": 10000,
"maxTime": "5:00:00"
},
"Picard_sortFinal": {
"memory": 5000,
"memory": 10000,
"maxTime": "5:00:00"
},
"Picard_cleanSamFinal": {
"memory": 5000,
"memory": 20000,
"maxTime": "5:00:00"
},
"Picard_FixMateInformationFinal": {
"memory": 15000,
"memory": 25000,
"maxTime": "5:00:00"
},
"Picardtools_MergeSamFiles": {
......@@ -105,27 +105,27 @@
"maxTime": "5:00:00"
},
"deepTools_computeGCBias": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"deepTools_correctGCBias": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"macs2_stringent": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"macs2_nonStringent": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"macs2_Encode": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"filterPeaks": {
"memory": 5000,
"memory": 10000,
"maxTime": "2:00:00",
"output": "/YOUR_DIRECTORY/output/LOGS_AND_BENCHMARKS/{rule}.out",
"error": "/YOUR_DIRECTORY/output/LOGS_AND_BENCHMARKS/{rule}.err"
......@@ -141,7 +141,7 @@
"maxTime": "5:00:00"
},
"stats": {
"memory": 5000,
"memory": 10000,
"maxTime": "10:00:00"
},
"bamCoverage": {
......@@ -150,19 +150,19 @@
},
"deepTools_plotCoverage": {
"memory": 10000,
"maxTime": "24:00:00"
"maxTime": "72:00:00"
},
"deepTools_plotCoverageMerged": {
"memory": 10000,
"maxTime": "24:00:00"
"maxTime": "72:00:00"
},
"deepTools_correlationPlots": {
"memory": 10000,
"maxTime": "24:00:00"
"maxTime": "72:00:00"
},
"deepTools_correlationPlotsPooledSamples": {
"memory": 10000,
"maxTime": "24:00:00"
"maxTime": "72:00:00"
},
"deepTools_plotPCA_peaksOnly": {
"memory": 10000,
......@@ -174,7 +174,7 @@
},
"deepTools_correlationPlotsPeaks": {
"memory": 10000,
"maxTime": "10:00:00"
"maxTime": "72:00:00"
},
"PCA_R": {
"memory": 10000,
......@@ -182,6 +182,6 @@
},
"multiqc": {
"memory": 10000,
"maxTime": "2:00:00"
"maxTime": "5:00:00"
}
}
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