revised fastqcreen

tasks/fastqscreen.wdl

@@ -3,8 +3,8 @@ task fastqscreen {
 	File read2
 	File screen_ref_dir
 	File fastq_screen_conf
-	String read1name = basename(read1,".fastq.gz")
-	String read2name = basename(read2,".fastq.gz")
+	String read1name = sub(basename(read1),"\\.\\S+$", "")
+	String read2name = sub(basename(read2),"\\.\\S+$", "")
 	String docker
 	String cluster
 	String disk_size