更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -7,6 +7,8 @@ task cnvkit{
     String? Ploidy
     File tumor_bam
     File tumor_bam_index
+    Array[File]? normal_bams
+    Array[File]? normal_bam_indexs
     File? normal_bam
     File? normal_bam_index
     String docker
@@ -29,6 +31,18 @@ task cnvkit{
        
        echo $center 
                   
+       if [ ${sep=" " normal_bams} ];then
+                   echo ${sep=" " normal_bams}
+                   /usr/local/bin/cnvkit.py target ${bed_file} --annotate ${ref_flat} --split --short-names -o my_baits.bed
+                   /usr/local/bin/cnvkit.py batch ${tumor_bam} \
+                      --normal ${sep=" " normal_bams} \
+                      --targets my_baits.bed \
+                      --fasta ${ref_dir} \
+                      --annotate ${ref_flat} -p $nt \
+                      --drop-low-coverage \
+                      --output-dir ${sample}.reference.cnn
+                  
+                  
        #WES
        if [ ${bed_file} ]; then
            echo "WES"