Reference.md

@@ -10,8 +10,8 @@ Snakemake uses wildcards and rules. Rules describe a shell command defined by in
 * **04_filter_samples** filters `projet`/`marker`/`run`/`sample` .fasta files
 * 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:
 
+Each workflow is stored with the following structure:
 ```
 ├── workflow
 │   ├── rules
@@ -38,23 +38,15 @@ Softwares and dependencies can be run directly on the local system or using envi
 
 [![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)
 
-We provide ready to run versions of container built with [Singularity containers](https://www.sylabs.io/). All required softwares to run the workflow have been installed within this container.
-
-User can either download the ready-to-use built container OR build this container instead to download it using the [Singularity.obitools](Singularity.obitools) recipe.
-
-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/)
-
+We provide ready to run versions of container built with [Singularity containers](https://www.sylabs.io/). All required softwares to run the workflow have been installed within this container. User can either download the ready-to-use built container OR build this container instead to download it using the [Singularity.obitools](Singularity.obitools) recipe. 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
 
 Softwares can be installed throught a conda environment. Each rule loads its own environment. Environment files are stored at `workflow/envs/obitools_envs.yaml`.
 
-
 # Wildcards
 
-Output and input can take any values. We defined them as wildcards.
-
-We use 4 wildcards:
+Output and input can take any values. We defined them as wildcards. We use 4 wildcards:
 
 * `projet`
 * `marker`
@@ -65,7 +57,6 @@ We use 4 wildcards:
 
 ## Overview
 
-
 ```mermaid
 
 graph TD;