Fix construction of cwltool command line

pvanheus · Oct 26, 2022 · b0adeb8 · b0adeb8
1 parent 8235a35
commit b0adeb8
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/lukasa.py b/lukasa.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import argparse
 import json
@@ -92,7 +92,10 @@ def is_fasta(input_filename):
         debug = "--debug"
     else:
         debug = ""
-    cwl_commandline = ["cwltool", "--no-container", debug, workflow_file, cwl_input_file.name]
+    cwl_commandline = ["cwltool", "--no-container"]
+    if args.debug:
+        cwl_commandline += ['--debug']
+    cwl_commandline += [workflow_file, cwl_input_file.name]
     workflow_output_str = subprocess.check_output(cwl_commandline)
 
     os.unlink(cwl_input_file.name)