perf(CNVkit): call filter

tasks/CNVkit.wdl

@@ -50,8 +50,9 @@ 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 call --drop-low-coverag --filter ci ${sample}.cns -y -m clonal --purity $PURITY -o ${sample}.call.cns
-    cnvkit.py call --drop-low-coverag --filter ci ${sample}.cnr -y -m clonal --purity $PURITY -o ${sample}.call.cnr
+    cnvkit.py ${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
     
     # Plot the results
     cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
@@ -60,8 +61,8 @@ task CNVkit {
     
     # Genemetrics
     mkdir gainloss
-    cnvkit.py genemetrics ${sample}.call.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
-    cnvkit.py genemetrics ${sample}.call.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
+    cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
+    cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
     # Filter genes
     cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
     cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt
@@ -70,7 +71,7 @@ task CNVkit {
     touch failed_genes.txt
     # for gene in `cat ${sample}.trusted_genes.txt`
     # do
-    #   cnvkit.py scatter ${sample}.call.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf || echo $gene >> failed_genes.txt
+    #   cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf || echo $gene >> failed_genes.txt
     # done
   >>>
   
@@ -88,7 +89,7 @@ task CNVkit {
     File cnr = "${sample}.cnr"
     File cns = "${sample}.cns"
     File stats = "${sample}.stats"
-    File call_cnr = "${sample}.call.cnr"
+    File call_cnr = "${sample}.cnr"
     File call_cns = "${sample}.call.cns"
     File ratio_cnv = "${sample}.ratio_cnv.txt"
     File segment_cnv = "${sample}.segment_cnv.txt"