ncbi · Jun 14, 2024
diff --git a/‎amr_naming/wf_amr_naming.cwl
-136 b/‎amr_naming/wf_amr_naming.cwl
-136
diff --git a/‎expr/supplemental_data_split_dir.cwl
-5 b/‎expr/supplemental_data_split_dir.cwl
-5
diff --git a/‎progs/amr_finder_plus.cwl
-45 b/‎progs/amr_finder_plus.cwl
-45
diff --git a/‎progs/amr_plus_adaptor.cwl
-30 b/‎progs/amr_plus_adaptor.cwl
-30
diff --git a/‎progs/asn_adjust.cwl
-26 b/‎progs/asn_adjust.cwl
-26
diff --git a/‎progs/map_amr_ids.cwl
-51 b/‎progs/map_amr_ids.cwl
-51
diff --git a/‎scripts/pgap.py
+2 b/‎scripts/pgap.py
+2
diff --git a/‎task_types/tt_amr_finder_plus.cwl
-53 b/‎task_types/tt_amr_finder_plus.cwl
-53
@@ -33,9 +33,6 @@ expression: |
         case 'AntiFamLib':
           r['AntiFamLib'] = l[i];
           break;
-        case 'AMRFinderPlus':
-          r['amr_finder_plus_database'] = l[i];
-          break;
         case 'asn2pas.xsl':
           r['asn2pas_xsl'] = l[i];
           break;
@@ -149,8 +146,6 @@ outputs:
     type: Directory
   all_order_specific_blastdb_file:
     type: File
-  amr_finder_plus_database:
-    type: File
   asn2pas_xsl:
     type: File
   identification_db_dir:
 
@@ -1183,6 +1183,8 @@ def main():
                 # see doubling down on it in previously exited def cleanup() method:
                 # 
                 list_to_delete = [args.input, 'input.yaml', 'pgap_input.yaml', 'submol.yaml']
+                if args.genome:
+                    list_to_delete.append()
                 for file in list_to_delete:
                     if file != None:
                         base =  os.path.basename(file)
Original file line number	Diff line number	Diff line change
`@@ -1183,6 +1183,8 @@ def main():`
`1183`	`1183`	`# see doubling down on it in previously exited def cleanup() method:`
`1184`	`1184`	`#`
`1185`	`1185`	`list_to_delete = [args.input, 'input.yaml', 'pgap_input.yaml', 'submol.yaml']`
	`1186`	`+ if args.genome:`
	`1187`	`+ list_to_delete.append()`
`1186`	`1188`	`for file in list_to_delete:`
`1187`	`1189`	`if file != None:`
`1188`	`1190`	`base = os.path.basename(file)`