Bugfix: workflow args were not passed to subprocess

This fixes bug introduced in #111.
ilastik · Aug 16, 2023 · f89e23e · f89e23e
1 parent 7b1e602
commit f89e23e
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/src/main/java/org/ilastik/ilastik4ij/workflow/WorkflowCommand.java b/src/main/java/org/ilastik/ilastik4ij/workflow/WorkflowCommand.java
@@ -92,8 +92,9 @@ private void runImpl(StatusBar status, Path inputDir, Path outputDir) {
 
         IlastikOptions opts = optionsService.getOptions(IlastikOptions.class);
         opts.load();
+
         List<String> args = commonSubprocessArgs(opts, projectFileName);
-        Map<String, String> env = subprocessEnv(opts);
+        args.addAll(workflowArgs());
 
         Map<String, Dataset> inputs = new HashMap<>(workflowInputs());
         inputs.put("raw_data", inputImage);
@@ -114,6 +115,7 @@ private void runImpl(StatusBar status, Path inputDir, Path outputDir) {
         Path outputPath = outputDir.resolve("predictions.h5");
         args.add("--output_filename_format=" + outputPath);
 
+        Map<String, String> env = subprocessEnv(opts);
         logger.info(String.format(
                 "Subprocess starting with arguments %s and environment %s", args, env));
         status.withSpinner("Running " + workflowName(), () -> {