更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -9,6 +9,7 @@ task cnvkit{
     File tumor_bam_index
     File? normal_bam
     File? normal_bam_index
+    File? VCF
     String docker
     String cluster_config
     String disk_size
@@ -95,8 +96,12 @@ task cnvkit{
                   -p $nt
                   
        ls ./
-       /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
-                  -o ${sample}.call.cns
+       if [ ${VCF} ]; then
+           /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center \
+                      -o ${sample}.call.cns
+       else
+            /usr/local/bin/cnvkit.py call ${sample}.cns/${sample}.cns --center-at $center --vcf ${VCF}\
+                      -o ${sample}.call.cns
                   
        
            # Plot the results