更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -7,8 +7,6 @@ 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
@@ -24,8 +22,6 @@ task cnvkit{
         
        echo ${sample}
                   
-       echo ${sep=" " normal_bams}
-                  
                   
        echo ${Ploidy}
        
@@ -33,17 +29,6 @@ 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
-       fi
                   
                   
        #WES