update instructions to run integration tests

README.md

@@ -143,20 +143,39 @@ If you get a 401 response to your API request with an `"Unauthorized: "` error m
 
 Neurobagel API utilizes [Pytest](https://docs.pytest.org/en/7.2.x/) framework for testing.
 
-To run the tests, first make sure you're in repository's main directory and in your environment where the dependencies are installed.
+To run the tests, first ensure you're in the repository's root directory and in the environment where the dependencies are installed.
 
-Next, make sure to launch the test SPARQL graph by:
+Install the submodules used by the tests:
+```bash
+git submodule init
+git submodule update
+```
+
+You can then run the tests by executing the following command in your terminal:
+
+```bash
+pytest tests
+```
+
+To run the integration tests of SPARQL queries (skipped by default), also launch the test graph store:
 
 ```bash
 docker compose up -d test_graph
 ```
 
-NOTE: Don't have a `.env` file in the root directory as it will conflict with the environment variable configuration of the docker compose file since docker compose will try to use that file by default.
+_NOTE: Don't have a `.env` file in the root directory as it will conflict with the environment variable configuration of the docker compose file, 
+since docker compose will try to use `.env` by default._
 
-You can then run the tests by executing the following command in your terminal:
+Then, run all tests using:
+```bash
+pytest -m "integration or not integration"
+# OR
+pytest -m ""
+```
 
+Or, to run only the integration tests:
 ```bash
-pytest tests
+pytest -m "integration"
 ```
 
 ## The default Neurobagel SPARQL query