revise qualimap

tasks/qualimap.wdl

@@ -11,10 +11,11 @@ task qualimap {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=10G
-		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
-		tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq
+		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
+		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=32G
 		tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
+		tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq
+		
 	>>>
 
 	runtime {
@@ -25,7 +26,7 @@ task qualimap {
 	}
 
 	output {
-		File rnaseq_gz = "${bamname}_rnaseq_qualimap.tar.gz"
 		File bamqc_gz = "${bamname}_bamqc_qualimap.tar.gz"
+		File rnaseq_gz = "${bamname}_rnaseq_qualimap.tar.gz"
 	}
 }