Reference.md

@@ -150,10 +150,21 @@ graph TD;
 
 ```
 
+## Description
 
+Summary, inputs, outputs of scripts. The scripts are ordered by steps
+
+* **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
+
+1. [Settings](###1-settings)
 
-## write demultiplex table
 
+### 1 Settings
 
 
 ```mermaid
@@ -192,6 +203,26 @@ Run : R2 .fastq.gz file path
 ```
 
 
+### 2 Assembly
+
+### 3 Demultiplexing
+
+
+### 4 Filtering
+
+### 5 Taxonomic assignment and format
+
+
+
+
+## write demultiplex table
+
+
+
+## 
+
+
+
 ### read 'rapidrun' .tsv file
 ### remove blacklisted runs & projects
 ### write table projet/run/sample