Changes to cluster.json

example/templates/cluster.json

@@ -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"
   }
 }