fastq screen filename match

.gitignore

@@ -0,0 +1,3 @@
+# jun shang samples test ignore
+choppy_samples.csv
+input_samples_test.txt

tasks/fastqscreen.wdl

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