Reference.md

@@ -157,12 +157,33 @@ Due to limitation of wildcards (at the demultiplexing and concatening steps, the
 * We concatenate  `projet`/`marker`/`run`/`sample` .fasta files into `projet`/`marker`/`run` .fasta files
 * **05_assignment** produces `projet`/`marker`/`run` species occurence table files
 
+Each workflow is stored with the following structure:
+
+```
+├── workflow
+│   ├── rules
+|   │   ├── module1.smk
+|   │   └── module2.smk
+│   ├── envs
+|   │   ├── tool1.yaml
+|   │   └── tool2.yaml
+|   └── Snakefile
+├── config
+│   └── config.yaml
+│
+└── results
+    └── workflow
+        ├── module1
+        └── module2
+```
+The workflow code goes into a subfolder `workflow`, while the configuration is stored in a subfolder `config`. Inside of the `workflow` subfolder, the central `Snakefile` marks the entrypoint of the workflow. Results are written into subfolder `results. Inside of the `results` subfolder, results are stored following the same structure than inside `workflow` subfolder.
 
-## Environment
+
+# Environment
 
 Softwares and dependencies can be run directly using environments such as containers or package management system.
 
-### Containers
+## Containers
 
 [![https://www.singularity-hub.org/static/simg/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2878)
 
@@ -173,8 +194,7 @@ User can either download the ready-to-use built container OR build this containe
 In both case, it gives an `obitools.simg` file. Absolute path to access to the container file fills the field `singularity:` into [config.yaml](config/)
 
 
-
-### Conda
+## Conda
 
 Softwares can be installed throught a conda environment. Each steps