new file: bcbio.rename_old_names.sh

	modified:   bcbio.templates.exome.yaml

bcbio.rename_old_names.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+#renames old runs of bcbio to annotated-decomposed.vcf.gz form
+
+if [ -z $family ];
+then
+    family=$1
+fi
+
+suffix="annotated-decomposed.vcf.gz"
+
+mv ${family}-ensemble.vcf.gz ${family}-ensemble-${suffix}
+mv ${family}-ensemble.vcf.gz.tbi ${family}-ensemble-${suffix}.tbi
+
+for tool in {platypus,freebayes,gatk-haplotype};
+do
+    mv ${family}-${tool}.decomposed.vcf.gz ${family}-${tool}-${suffix}
+    mv ${family}-${tool}.decomposed.vcf.gz.tbi ${family}-${tool}-${suffix}.tbi
+done

bcbio.templates.exome.yaml

@@ -26,7 +26,7 @@ details:
     batch: 166
 resources:
   default:
-    cores: 5
+    cores: 7
     jvm_opts:
     - -Xms750m
     - -Xmx7000m