command line

tasks/NGScheckMates.wdl

@@ -10,8 +10,7 @@ task NGScheckMates {
 		set -e
 		nt=$(nproc)
 		export NCM_HOME=/opt/NGSCheckMate
-		python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -nz
-		ls /cromwell_inputs/* > wd.txt
+		python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -nz -s 0.5
 	>>>
 
 	runtime {