fastq screen filename match

tasks/fastqscreen.wdl

@@ -13,8 +13,8 @@ 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 {