Reference.md

@@ -309,23 +309,51 @@ We concatenate  `projet`/`marker`/`run`/`sample` .fasta files into `projet`/`mar
 
 #### 5.1. Dereplicate sequences at `run` level
 
+[dereplicate_runs](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/rules/dereplicate_runs.smk): dereplicate sequences
+
+* input:
+    * results/05_assignment/01_runs/`run`.fasta : concatenated `sample` into `run` sequences .fasta file
+* output:
+   * results/05_assignment/02_dereplicated/`run`.uniq.fasta: dereplicated sequences .fasta file
 
 
 #### 5.2. Taxonomic assignment
 
-Assign each sequence to a taxon
+[assign_taxon](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/rules/assign_taxon.smk): assign each sequence to a taxon
+
+* inputs:
+   * results/05_assignment/02_dereplicated/`run`.uniq.fasta: dereplicated sequences .fasta file
+   * `marker` reference database taxonomy files: EMBL format reference database with taxonomy information
+   * `marker` reference database fasta file: list of reference sequences for each taxa
+* output:
+   * results/05_assignment/03_assigned/`run`.tag.u.fasta: taxon assigned sequences .fasta file
 
 #### 5.3. Remove not relevant attributes
 
-Some attributes can be removed at this stage
+[rm_attributes](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/rules/rm_attributes.smk): some attributes can be removed at this stage
+
+* input:
+   * results/05_assignment/03_assigned/`run`.tag.u.fasta: taxon assigned sequences .fasta file
+* output:
+   * results/05_assignment/04_formated/`run`.a.t.u.fasta: cleaned .fasta file
 
 #### 5.4. Sort sequences
 
-The sequences can be sorted by decreasing order of count
+[sort_runs](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/rules/sort_runs.smk): the sequences are sorted by decreasing order of count.
+
+* input:
+   * results/05_assignment/04_formated/`run`.a.t.u.fasta: cleaned .fasta file
+output:
+   * results/05_assignment/04_formated/`run`.s.a.t.u.fasta: sorted .fasta file
 
 #### 5.5. Generate species occurrence final tables
 
-Generate a table final results
+[table_runs](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/05_assignment/rules/table_runs.smk): converts sequence .fasta file to a tabular file that can be open by a spreadsheet program.
+
+* input:
+   * results/05_assignment/04_formated/`run`.s.a.t.u.fasta: sorted .fasta file
+* output:
+   * results/06_final_tables/`run`.csv: species occurrence .csv file