read2

tasks/fastqscreen.wdl

 task fastq_screen {
 	File read1
-	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
 		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}
 	>>>
 
 	runtime {
 		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"
 	}
 }