add-cluster

tasks/trimmomatic.wdl

@@ -7,7 +7,7 @@ task trimmomatic {
 	String cluster
 
 	command {
-  	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${baseout} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
+  	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  ${baseout}_1P.fq.gz ${baseout}_2P.fq.gz ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
 	}
 
 	runtime {
@@ -18,7 +18,7 @@ task trimmomatic {
 	}
 
 	output {
-		File read_1p = "${baseout}/${baseout}_1P.fq.gz"
-		File read_2p = "${baseout}/${baseout}_2P.fq.gz"
+		File read_1p = "${baseout}_1P.fq.gz"
+		File read_2p = "${baseout}_2P.fq.gz"
 	}
 }