更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -104,7 +104,7 @@ task cnvkit{
        
          
         #gain and loss
-        cat ${sample}.call.cns > ${sample}.call.cns.bed
+        /root/miniconda2/bin/cnvkit.py export vcf ${sample}.call.cns -y -i "${sample}" -o ${sample}.call.cns.vcf
                 
 
         tar cvf ${sample}.tar ${sample}*
@@ -121,7 +121,7 @@ task cnvkit{
 
     output{
         File out_file = "${sample}.tar"
-        File cnv_bed = "${sample}.call.cns.bed"
+        File cnv_bed = "${sample}.call.cns.vcf"
     }
 
 }