Merge branch 'fix-output-dir-issue' into 'main'

Fix output dir issue

See merge request !5

run_tests.py

+#!/usr/bin/env python
 import unittest
 
 #Run all tests

src/workflow.py

@@ -6,6 +6,7 @@ from . import constant
 import os
 import re
 import json
+from pathlib import Path
 
 
 class Workflow:
@@ -14,7 +15,13 @@ class Workflow:
                  license = None, creativeWorkStatus = None, authors = None, 
                  version = None, keywords = None, producer = None,
                  publisher = None):
-        self.nextflow_file = Nextflow_File(file, duplicate = duplicate, display_info = display_info)
+        self.nextflow_file = Nextflow_File(
+            file,
+            duplicate=duplicate,
+            display_info=display_info,
+            output_dir=output_dir
+        )
+        self.output_dir = Path(output_dir)
         self.rocrate = None
         self.name = name
         self.datePublished = datePublished

tests/test_cli.py

+import pathlib
+import unittest
+from tempfile import TemporaryDirectory
+
+from bioflow_insight_cli.main import cli
+
+
+class TestCall(unittest.TestCase):
+
+    def test_cli_works(self):
+        cli("./wf_test/main.nf", render_graphs=True)
+        cli("./wf_test/main.nf", render_graphs=False)
+
+    def test_cli_output_considered(self):
+        with TemporaryDirectory() as my_temp_dir:
+            my_results = pathlib.Path(my_temp_dir) / "my_results"
+            self.assertFalse(my_results.exists())
+            cli("./wf_test/main.nf", render_graphs=False, output_dir=str(my_results))
+            self.assertTrue(my_results.exists(), "Results should be there, output_dir not taken into account")
+