Update 'tasks/fastqscreen.wdl'

output file names from fastq.gz and fq.gz

tasks/fastqscreen.wdl

@@ -3,8 +3,6 @@ task fastq_screen {
 	File read2
 	File screen_ref_dir
 	File fastq_screen_conf
-	String read1name = basename(read1,".fastq.gz")
-	String read2name = basename(read2,".fastq.gz")
 	String docker
 	String cluster_config
 	String disk_size
@@ -15,22 +13,23 @@ task fastq_screen {
 		nt=$(nproc)
 		mkdir -p /cromwell_root/tmp
 		cp -r ${screen_ref_dir} /cromwell_root/tmp/
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${read1}
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${read2}
 	>>>
 
 	runtime {
 		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
+	
 	output {
-		File png1 = "${read1name}_screen.png"
-		File txt1 = "${read1name}_screen.txt"
-		File html1 = "${read1name}_screen.html"
-		File png2 = "${read2name}_screen.png"
-		File txt2 = "${read2name}_screen.txt"
-		File html2 = "${read2name}_screen.html"
+		File png1 = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_screen.png")
+		File txt1 = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_screen.txt")
+		File html1 = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_screen.html")
+		File png2 = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_screen.png")
+		File txt2 = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_screen.txt")
+		File html2 = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_screen.html")
 	}
 }