fix(CNVkit): output

tasks/CNVkit.wdl

 task CNVkit {
-
+  
   String sample
   File ref_dir
   String fasta
     # 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
-    
+    cnvkit.py call ${sample}.cnr -y -m clonal --purity $PURITY -o ${sample}.call.cnr
+
     # Plot the results
     cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}.scatter.pdf
     cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
     
     # Genemetrics
     mkdir gainloss
-    cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0 -m 0 -o ${sample}.cnv.txt
+    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
     # Filter genes
-    cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio-genes.txt
-    cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment-genes.txt
-    cat ${sample}.ratio-genes.txt | tail -n+2 | cut -f1 | sort | uniq > ratio-genes.txt
-    cat ${sample}.segment-genes.txt | tail -n+2 | cut -f1 | sort | uniq > segment-genes.txt
-    comm -12 ratio-genes.txt segment-genes.txt > ${sample}.trusted_cnv_genes.txt
-    for gene in `cat ${sample}.trusted_cnv_genes.txt`
+    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
+    comm -12 ratio_cnv.txt segment_cnv.txt > ${sample}.trusted_genes.txt
+    for gene in `cat ${sample}.trusted_genes.txt`
     do
-      cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf
+      cnvkit.py scatter ${sample}.call.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf
     done
   >>>
   
     File cnr = "${sample}.cnr"
     File cns = "${sample}.cns"
     File stats = "${sample}.stats"
+    File call_cnr = "${sample}.call.cnr"
     File call_cns = "${sample}.call.cns"
-    File genemetrics = "${sample}.cnv.txt"
-    File gainloss_genes = "${sample}.trusted_cnv_genes.txt"
+    File ratio_cnv = "${sample}.ratio_cnv.txt"
+    File segment_cnv = "${sample}.segment_cnv.txt"
+    File gainloss_genes = "${sample}.trusted_genes.txt"
     Array[File] gainloss = glob("./gainloss/*")
   }
 }