fix bug

tasks/qualimap.wdl

@@ -11,7 +11,8 @@ task qualimap {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/opt/qualimap/qualimap bamqc -bam ${bam} -gff ${regions} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G 
+		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}
 	>>>