Reference.md

@@ -54,7 +54,7 @@ graph TD;
   classDef Snakefile fill:#98FB98,border:#0c4c0c;
  
  
-  id0a{{rapidrun.tsv}}-->s0;
+  id0a{{rapidrun.csv}}-->s0;
   id0s{{`marker` sample description .dat}}-->s0;
   id0c{{config.yaml}}-->s0;
  
@@ -136,7 +136,7 @@ graph TD;
 
   click id0c "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/config";
   click id0b "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/results/01_settings"
-  click id0a "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.tsv";
+  click id0a "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.csv";
   click id0s "https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/resources/test/sample_description";
 
   
@@ -163,7 +163,7 @@ The [config file](config/) defines a dictionary of configuration parameters and
 | parameters | descriptions | softwares | rules | default values | excepted type |
 |------------|--------------|-----------|-------|-----------|--------------------|
 | singularity                    | absolute path of singularity container file [![https://www.singularity-hub.org/static/simg/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/2878) | [singularity](https://singularity.lbl.gov/) | every rules need this container to work | /workdir/conteneur/obitools.simg | absolute path file |
-| fichiers: rapidrun              | absolute path of the rapidrun .tsv file | [readwrite_rapidrun_demultiplexing](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/01_settings/readwrite_rapidrun_demultiplexing.py) | settings | resources/test/all_samples.tsv | absolute path file |
+| fichiers: rapidrun              | absolute path of the rapidrun .csv file | [readwrite_rapidrun_demultiplexing](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/01_settings/readwrite_rapidrun_demultiplexing.py) | settings | resources/test/all_samples.csv | absolute path file |
 | fichiers: folder_fastq          | absolute path of a folder which contains pairend-end raw reads .fastq.gz |  [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend) | illuminapairedend | /workdir/ngs/ | absolute path folder |
 | dat: `marker`                   | absolute path of `marker` sample description .dat file | [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) | assign_sequences | resources/test/sample_description/`marker`.dat | dictionnary `marker`: absolute path of file |
 | blacklist: projet               | list of `projet` to exclude from the analysis | [readwrite_rapidrun_demultiplexing](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/01_settings/readwrite_rapidrun_demultiplexing.py) | settings | dummy_projet | `projet` wildcards value |
@@ -183,7 +183,7 @@ The [config file](config/) defines a dictionary of configuration parameters and
 * inputs:
   * [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.
   * [config.yaml](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/config): see configuration step
-  * [rapidrun.tsv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/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.
+  * [rapidrun.csv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.csv) : 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](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/tree/master/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.
 
@@ -223,7 +223,7 @@ Run : R2 .fastq.gz file path
 
 ### 2. Assembly
 
-The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/Snakefile) will use the wildcards `run` deduced from [rapidrun.tsv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.tsv) and performs the following rules:
+The [assembly Snakefile](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/02_assembly/Snakefile) will use the wildcards `run` deduced from [rapidrun.csv](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/blob/master/resources/test/all_samples.csv) and performs the following rules:
 
 #### 2.1 Align and merge paired-end reads