test folder

README.md

@@ -21,7 +21,7 @@ OTU-clustering steps are based on [TARA Fred's metabarcoding pipeline](https://g
 
 ![ednaotucluster](docs/edna_otucluster_workflow.png)
 
-1. [Installation]()
+1. [Installation](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home#installation)
 2. Pipeline configuration
     * [Local installation]()
     * [Adding your own system config]()
@@ -39,6 +39,40 @@ OTU-clustering steps are based on [TARA Fred's metabarcoding pipeline](https://g
 6. [Reference]()
 7. [Metabarcoding context - discussion to go further]()
 
+## Quick Start
+
+See [Install section](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home#installation) for installation instructions.
+
+Download example data:
+
+```
+curl -JLO http://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_data_test/-/raw/master/test_rapidrun_data.tar.gz; tar zfxz test_rapidrun_data.tar.gz -C resources/test/
+```
+
+`./resources/test/test_rapidrun_data/`: this folder contains a reference database for 4 markers (Teleo01; Mamm01; Vert01; Chond01), NGS metabarcoding raw data, required metadata to handle demultiplexing on RAPIDRUN format.
+
+If you have installed **eDNA-seq Metabarcoding OTU-clustering**, you can run the example data with:
+
+```
+snakemake --configfile config/config_test_rapidrun.yaml --cores 4 --use-conda
+```
+
+This will generate outputs into `./results` folder.
+
+OTU tables are available as `.csv` file while intermediates files are stored into `./results/intermediates` folder.
+
+```
+intermediates                       projet1_mamm_ecotag_ncbi_motu.csv   projet1_teleo_table_motu.csv
+projet1_chond_ecotag_ncbi_motu.csv  projet1_mamm_table_motu.csv         projet1_vert_ecotag_ncbi_motu.csv
+projet1_chond_table_motu.csv        projet1_teleo_ecotag_ncbi_motu.csv  projet1_vert_table_motu.csv
+```
+
+## Next steps
+
+Now that you've gotten the example to work, see the [wiki](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home) to navigate to the more detailed descriptions and instructions for exploring your own data.
+
+
+
 ## Credits
 
 **eDNA-seq Metabarcoding OTU-clustering** was coded and written by Virginie Marques and Pierre-Edouard Guerin.