更新 'tasks/batch.wdl'

tasks/batch.wdl

@@ -2,7 +2,6 @@ task batch {
     String sample_id
     Array[File] tumor_bam
     Array[File] normal_bam
-    File bed
     File faidx
     File fasta
     File? ref_flat
@@ -39,13 +38,15 @@ task batch {
         mkdir results
         cnvkit.py batch -p $nt ${sep=' ' tumor_bam} --normal ${sep=' ' normal_bam} \
         --method ${method} --segment-method ${segment_method} \
-        --targets target.bed ${access_opt} ${annotate_opt} \
+        ${access_opt} ${annotate_opt} \
         --fasta hg_ref.fa ${reference_opt} \
         --output-reference ${sample_id}.reference.cnn \
         --output-dir ./results/ \
         --drop-low-coverage --diagram --scatter
         
         cp ${sample_id}.reference.cnn ~/${sample_id}.reference.cnn
+                    
+        
     >>>
 
     runtime {