Commit 94f20f20 authored by peguerin's avatar peguerin
Browse files

test folder

parent 77ef0f5a
......@@ -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.
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