Update README.md

README.md

@@ -11,29 +11,34 @@ This template contains a mock analysis pipeline with some mock data:
  * 2 figures
 
 ## Running the analysis pipeline
-* Download the study template by clicking [here](https://github.com/AaltoImagingLanguage/study_template/archive/master.zip)
-* Extract the downloaded zip file
-* Open a terminal and move into the folder containing the study template
-* Make sure all required python packages are installed by running: `pip install -r requirements.txt`
-* Run the analysis by either:
-  * run `doit` to use a build system to run all the analysis steps
-  * alternatively, run `python master.py` to use a simple master script to run all the analysis steps
+1. Download the study template by clicking [here](https://github.com/AaltoImagingLanguage/study_template/archive/master.zip)
+1. Extract the downloaded zip file
+1. Open a terminal and move into the folder containing the study template
+1. Make sure all required python packages are installed by running: `pip install -r requirements.txt`
+
+1. Run the analysis by either:
+   * run `doit` to use a build system to run all the analysis steps
+   * alternatively, run `python master.py` to use a simple master script to run all the analysis steps
 
 After the analysis has been completed:
  * the processed data should be in the `processed/` folder
  * the HTML reports should be in the `reports/` folder
  * the generated figures should be in the `figures/` folder.
 
 ## Getting started with a new data analysis pipeline based on the study template
-* Download the study template by clicking [here](https://github.com/AaltoImagingLanguage/study_template/archive/master.zip)
-* Extract the downloaded zip file
-* Modify `config.py`
-  * Add your system to the list at the top, indication where your data is, how many cores you have on your machine, etc.
-  * Add all parameters relevant to your analysis to the script
-  * Add all filenames relevant to your analysis to the script
-* Add new scripts for each analysis step and each figure
-* Modify the master script to execute the scripts you have added by either:
-  * Add new tasks to the `dodo.py` script to use the `doit` build system to run all the analysis steps. Delete `master.py`.
-  * alternatively, add new lines to execute the scripts you have added to the `master.py` file to use a simple master script to run all the analysis steps. Delete `dodo.py`.
-* Modify `requirements.txt`
-  * Add all python packages your analysis pipeline needs
+1. Download the study template by clicking [here](https://github.com/AaltoImagingLanguage/study_template/archive/master.zip)
+1. Extract the downloaded zip file
+
+1. Modify `config.py`
+   1. Add your system to the list at the top, indication where your data is, how many cores you have on your machine, etc.
+   1. Add all parameters relevant to your analysis to the script
+   1. Add all filenames relevant to your analysis to the script
+
+1. Add new scripts for each analysis step and each figure
+
+1. Modify the master script to execute the scripts you have added by either:
+   * Add new tasks to the `dodo.py` script to use the `doit` build system to run all the analysis steps. Delete `master.py`.
+   * alternatively, add new lines to execute the scripts you have added to the `master.py` file to use a simple master script to run all the analysis steps. Delete `dodo.py`.
+
+1. Modify `requirements.txt`
+   1. Add all python packages your analysis pipeline needs