更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -37,6 +37,8 @@ task cnvkit{
         awk 'NR==FNR {a[$1]=$2;next} NR!=FNR {if(FNR == 1 || (FNR != 1 && $1 in a)) print $0}' ${sample}.trusted_genes.txt ${sample}.ratio_cnv.txt > ${sample}.ratio_cnv.trusted.txt
         /root/miniconda2/bin/cnvkit.py call ${sample}.ratio_cnv.trusted.txt -m threshold -o ${sample}.ratio_cnv.call.txt
         awk '{if ($6 != 2) print $0}' ${sample}.ratio_cnv.call.txt > ${sample}.ratio_cnv.call.filter.txt
+        
+        cp ${sample}.ratio_cnv.call.filter.txt ${sample}.ratio_cnv.call.filter.bed
 
         ls ./
 
@@ -53,6 +55,7 @@ task cnvkit{
 
     output{
         File out_file = "${sample}.tar"
+        File cnv_bed = "${sample}.ratio_cnv.call.filter.bed"
     }
 
 }