Merge pull request #90 from swisstopo/feature-README.md-update

Update Run data extraction instruction

README.md

@@ -103,13 +103,14 @@ To execute the data extraction pipeline, follow these steps:
 
     The main script for the extraction pipeline is located at `src/stratigraphy/main.py`. A cli command is created to run this script.
 
-    Run `boreholes-extract-all` to run the main extraction script. With the default options, the command will source all PDFs from the `data/Benchmark` directory and create PNG files in the `data/Benchmark/extract` directory.
+    Run `boreholes-extract-all` to run the main extraction script. You need to specify the input directory or a single PDF file using the `-i` or `--input-directory` flag. 
+ The script will source all PDFs from the specified directory and create PNG files in the `data/output/draw` directory.
 
     Use `boreholes-extract-all --help` to see all options for the extraction script.
 
 4. **Check the results**
 
-    Once the script has finished running, you can check the results in the `data/Benchmark/extract` directory. The result is a `predictions.json` file as well as a png file for each page of each PDF in the `data/Benchmark` directory.
+    Once the script has finished running, you can check the results in the `data/output/draw` directory. The result is a `predictions.json` file as well as a png file for each page of each PDF in the specified input directory.
 
 ### Output Structure
 The `predictions.json` file contains the results of a data extraction process from PDF files. Each key in the JSON object is the name of a PDF file, and the value is a list of extracted items in a dictionary like object. The extracted items for now are the material descriptions in their correct order (given by their depths).