fix(CNVkit): call.cnr

tasks/CNVkit.wdl

@@ -51,8 +51,8 @@ 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 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
+    cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns
+    cnvkit.py call ${sample}.cnr --drop-low-coverage -m threshold --purity $PURITY -o ${sample}.call.cnr
     
     # Plot the results
     cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
@@ -89,7 +89,7 @@ task CNVkit {
     File cnr = "${sample}.cnr"
     File cns = "${sample}.cns"
     File stats = "${sample}.stats"
-    File call_cnr = "${sample}.cnr"
+    File call_cnr = "${sample}.call.cnr"
     File call_cns = "${sample}.call.cns"
     File ratio_cnv = "${sample}.ratio_cnv.txt"
     File segment_cnv = "${sample}.segment_cnv.txt"