更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -5,7 +5,7 @@ task cnvkit{
     String? fasta
     File ref_flat
     File bed_file
-    String center_at
+    File hrd
     File tumor_bam
     File tumor_bam_index
     File? normal_bam
@@ -22,8 +22,10 @@ task cnvkit{
        nt=$(nproc)
         
        echo ${sample}
+                  
+       PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
        
-       center=`awk -v vv=${center_at} 'BEGIN {print log(2/vv)/log(2)}'`
+       center=`awk -v vv=$PURITY 'BEGIN {print log(2/vv)/log(2)}'`
        
        echo $center