add-cluster

tasks/trimmomatic.wdl

@@ -3,12 +3,11 @@ task trimmomatic {
 	File read2
 	File adapter
 	String baseout
-	String baseout_gz = baseout + ".fq.gz"
 	String docker
 	String cluster
 
 	command {
-  	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${baseout_gz} ILLUMINACLIP:${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 ${baseout} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
 	}
 
 	runtime {