command line

tasks/NGScheckMates.wdl

@@ -11,8 +11,7 @@ task NGScheckMates {
 		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
-		pwd > wd.txt
-		ls >> wd.txt
+		ls /cromwell_inputs/ > wd.txt
 	>>>
 
 	runtime {
@@ -23,8 +22,7 @@ task NGScheckMates {
 	}
 	output {
 		File all_txt="output_all.txt"
-		File ncm="RiboZero_D5_1.ncm"
-		File loc="wd.txt"
+		File ncm="wd.txt"
 		File cor_txt="output_corr_matrix.txt"
 		File matched_txt="output_matched.txt"
 		File r_script="r_script.r"