fix(CNVkit): purity

tasks/CNVkit.wdl

@@ -51,10 +51,10 @@ task CNVkit {
     
     # Check noise
     cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
-
+    
     # Derive each segment's absolute integer copy number, ploidy must be int value
-    purity=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
-    cnvkit.py call ${sample}.cns -y -m clonal --purity ${purity} -o ${sample}.call.cns
+    PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
+    cnvkit.py call ${sample}.cns -y -m clonal --purity $PURITY -o ${sample}.call.cns
     
     # Plot the results
     cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf