fix(CNVkit): segmetrics

tasks/CNVkit.wdl

@@ -50,7 +50,7 @@ task CNVkit {
     
     # 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 ${sample}.cns --ci --sem -o ${sample}.segmetrics.cns
+    cnvkit.py segmetrics ${sample}.cns --ci --sem -o ${sample}.segmetrics.cns
     cnvkit.py call --drop-low-coverag --filter ci --filter sem ${sample}.segmetrics.cns -y -m clonal --purity $PURITY -o ${sample}.call.cns
     # cnvkit.py call --drop-low-coverag ${sample}.cnr -y -m clonal --purity $PURITY -o ${sample}.cnr