From f89e23e04fb5dc47fd2882c591f002933805b8c6 Mon Sep 17 00:00:00 2001
From: Emil Melnikov <emilmelnikov@gmail.com>
Date: Wed, 16 Aug 2023 14:55:04 +0200
Subject: [PATCH] Bugfix: workflow args were not passed to subprocess

This fixes bug introduced in https://github.com/ilastik/ilastik4ij/pull/111.
---
 .../java/org/ilastik/ilastik4ij/workflow/WorkflowCommand.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/ilastik/ilastik4ij/workflow/WorkflowCommand.java b/src/main/java/org/ilastik/ilastik4ij/workflow/WorkflowCommand.java
index ead8ea07..37bd1bc5 100644
--- 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(), () -> {