更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -4,6 +4,7 @@ task cnvkit{
     File ref_dir
     String? fasta
     File ref_flat
+    File bed_file
     File tumor_bam
     File tumor_bam_index
     File? normal_bam
@@ -26,7 +27,7 @@ task cnvkit{
                   --method wgs \
                   --fasta ${ref_dir} \
                   --annotate ${ref_flat} -p $nt \
-                  --targets targets.bed \
+                  --targets ${bed_file} \
                   --drop-low-coverage \
                   --output-dir ${sample_id}.reference.cnn