fix runner

mskcc · May 4, 2018 · 63025b8 · 63025b8
1 parent 0648b04
commit 63025b8
Showing 1 changed file with 6 additions and 3 deletions.
diff --git a/python_tools/pipeline_kickoff/pipeline_runner.py b/python_tools/pipeline_kickoff/pipeline_runner.py
@@ -144,9 +144,7 @@ def run_toil(args, output_directory, jobstore_path, logdir, unknowns):
         '--batchSystem', args.batch_system,
         '--workDir', output_directory,
         '--outdir', output_directory,
-        '--writeLogs', logdir,
-        args.workflow,
-        args.inputs_file
+        '--writeLogs', logdir
     ])
 
     ARG_TEMPLATE = ' {} {} '
@@ -160,6 +158,11 @@ def run_toil(args, output_directory, jobstore_path, logdir, unknowns):
     if len(unknowns) > 0:
         cmd += ' '.join(unknowns)
 
+    cmd += ARG_TEMPLATE.format(
+        args.workflow,
+        args.inputs_file
+    )
+
     print "Running Toil with command: {}".format(cmd)
     subprocess.check_call(cmd, shell=True)