更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -102,7 +102,9 @@ task cnvkit{
     	/root/miniconda2/bin/cnvkit.py diagram ${sample}.cns/${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
     	/root/miniconda2/bin/cnvkit.py heatmap ${sample}.cns/${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
        
-        cp ${sample}.call.cns ${sample}.call.cns.bed
+         
+        #gain and loss
+        cat ${sample}.call.cns | awk -v OFS='\t' '{ if ($6 > 2) print $0, "gain"; else if ($6 < 2) print $0, "loss"; else print $0 }' > ${sample}.call.cns.bed