fix(CNVkit): segmetrics

tasks/CNVkit.wdl

     
     # 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 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
+    cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns
+    cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m clonal --purity $PURITY -o ${sample}.call.cns
+    # cnvkit.py call --drop-low-coverag ${sample}.cnr -m clonal --purity $PURITY -o ${sample}.cnr
     
     # Plot the results
     cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf