add some documentation about the workflow

README.md

@@ -1,10 +1,34 @@
-# Master Thesis at UiO workflow
-Snakemake workflow for processing FLEXPART and FLEXDUST model output and doing analysis related to my thesis.
+# Snakemake Workflow for preprossing of FLEXPART and FLEXDUST output
 
+The workflow expect the output format to be accoring to model setup using the [FLEXPART-script](https://github.com/MasterOnDust/FLEXPART-script) python command line tool.  
 
-Includes both workflow for processing ERA5 data using snakemake and FLEXPART/FLEXDUST model ouput.
+### Installation
 
-- Can calculate a variety of different atmoshperic indicies from monthly ERA5 data.
-- Flexible and can be easily extended 
+1. Setup conda enviroment
+```shell
+conda env create -p ./dust -f environment.yml 
+```
+Activate conda enviroment
 
-Created by Ove Haugvaldstad 
+```shell
+conda activate ./dust
+```
+
+### Running the workflow
+
+The workflow can be configured in the `config/config.yaml` file. Most important is to set the paths correctly. 
+
+1. Test that all the files are there:
+
+```
+snakemake -n make_source_contrib_march
+```
+
+2. If snakemake is able to resolve all the paths then run the workflow by:
+```
+snakemake -j2 make_source_contrib_march
+```
+
+Please have look at what the rules does in the Snakefile. 
+
+If you have questions about how about this setup and want to setup a similar workflow the please get in touch at [email protected]