fix bug

tasks/qualimapBAMqc.wdl

@@ -11,8 +11,9 @@ task qualimapBAMqc {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/opt/qualimap/qualimap bamqc -bam ${bam} -regions ${regions} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
-		tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
+		awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${regions} > new.bed
+		/opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G 
+		tar -zcvf ${bamname}_qualimap.zip ${bamname}
 	>>>
 
 	runtime {