Reference.md

@@ -241,14 +241,22 @@ The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidr
 
 #### 3.1. Assign each sequence record to the corresponding `sample`
 
-[assign_sequences](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/03_demultiplex/rules/assign_sequences.smk): assign each sequence record to the corresponding `projet`/`marker`/run`/`plaque` == `sample`
+[assign_sequences](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/03_demultiplex/rules/assign_sequences.smk): assign each sequence record to the corresponding `projet`/`marker`/`run`/`sample`
 
 * inputs:
   * results/02_assembly/02_remove_unaligned/`run`.ali.fastq: aligned and merged sequences fastq file
-  * `marker` sample description .dat file
+  * [sample description .dat files](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/resources/test/sample_description): a table with 6 columns (plaque, plaque1, barcode, primer5, primer3, infos) and rows as a `plaque` element description. Each sample description file belong to a `marker` wildcard.
 * output:
-  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/run`.ali.assigned.fastq
+  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/`run`.ali.assigned.fastq
+
+###  3.2 Split `run` file into `run`/`sample` files
+
+[split_sequences](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/03_demultiplex/rules/split_sequences.smk): split the input sequence file in a set of subfiles according to the values of attribute `sample`
 
+* input:
+  * results/03_demultiplex/01_assign_sequences/`projet`/`marker`/`run`.ali.assigned.fastq
+* output:
+  * results/03_demultiplex/02_raw/`projet`/`marker`/`run`/`sample`.fasta
 
 
 ### 4 Filtering