fix bugs

README.md

@@ -0,0 +1,2 @@
+# NGS Check mates
+

tasks/NGScheckMates.wdl

@@ -3,7 +3,6 @@ task NGScheckMates {
 	File input_file
 	File out_dir
 	String docker
-	String out_dir = "./"
 	String cluster_config
 	String disk_size
 
@@ -11,7 +10,7 @@ task NGScheckMates {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		python ncm_fastq.py -l ${input_file} -pt SNP/SNP.pt –O ${out_dir} -p $nt -s 0.3 -f
+		python ncm_fastq.py -l ${input_file} -pt SNP/SNP.pt –O ./ -p $nt -s 0.3 -f
 	>>>
 
 	runtime {