Reference.md

@@ -176,13 +176,13 @@ The [config file](config/) defines a dictionary of configuration parameters and
 
 [01_settings/readwrite_rapidrun_demultiplexing.py](01_settings/readwrite_rapidrun_demultiplexing.py): write the demultiplex.csv file that the Snakefiles will read to define their wildcards.
 * inputs:
-  * [sample description .dat files](resources/test/sample_description)
-  * [config.yaml](config/)
-  * [rapidrun.tsv](resources/test/all_samples.tsv)
+  * [sample description .dat files](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.
+  * [config.yaml](config/): see configuration step
+  * [rapidrun.tsv](resources/test/all_samples.tsv) : a table with 5 columns (plaque, run, sample, projet ,marker) and rows as `projet`/`marker`/`run`/`plaque`==`sample` element description.
 * output:
-  * [results/01_settings/demultiplexing.csv](results/01_settings)
+  * [results/01_settings/demultiplexing.csv](results/01_settings) : a dataframe with 14 columns (demultiplex, projet, marker, run, plaque, sample ,barcode5, barcode3 , primer5, primer3, min_f, min_r, lenBarcode5, lenBarcode3) and rows as `projet`/`marker`/`run`/`plaque`==`sample` element description.
+
 
-:page_facing_up: [results/01_settings/demultiplexing.csv](results/01_settings) has