readme and fixes

README.md

@@ -6,4 +6,23 @@ To generate a new structure using this template, run
 
 with path pointing to the desired output directory.
 
-You will get the following structure:
+You will get the following structure:
+
+    ├── copier.yml
+    ├── README.md
+    ├── .template
+    │   ├── config
+    │   │   └── config.yaml.tmpl
+    │   └── workflow
+    │       └── Snakefile.tmpl
+    └── workflow
+        ├── rules
+        │   └── common.smk
+        └── Snakefile
+
+The `workflow` folder contains the structure to put the actual workflow in.
+Make sure to follow the [best practices](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility).
+
+The `.template` folder contains an automatically generated template for deploying the workflow using Snakemake's [module system](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#snakefiles-modules).
+Here, you should edit the `config.yaml.tmpl` to contain the config settings you would like to initialize in the deployment of the user.
+It is possible to add further files needed for the configuration to the `.template` folder, e.g. sample sheets.