Reference.md

@@ -146,6 +146,17 @@ graph TD;
 
 We use [snakemake](https://snakemake.readthedocs.io/en/stable/), a workflow management system to create scalable and reproducible metabarcoding analysis.
 
+Snakemake uses wildcards and rules. Rules describe a shell command defined by input and output variables. Wildcards describe the generalization of the values taking by input and output variables.
+
+Due to limitation of wildcards (at the demultiplexing and concatening steps, the workflow is splitted into 5 snakemake workflow.
+
+* **01_settings** produces the table to define wildcards
+* **02_assembly** merges `run` paired-end .fastq files
+* **03_demultiplex** generates `projet`/`marker`/`run`/`sample` .fasta files from `run` merged .fastq files 
+* **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
+
 
 ## Environment
 
@@ -165,6 +176,10 @@ In both case, it gives an `obitools.simg` file. Absolute path to access to the c
 
 ### Conda
 
+Softwares can be installed throught a conda environment. Each steps 
+
+04_filter_samples/envs/obitools_envs.yaml
+
 
 ## Wildcards