Commit 9ae43072 authored by peguerin's avatar peguerin
Browse files

readme update

parent dbdc4469
...@@ -8,7 +8,7 @@ OTU clustering based on [TARA Fred's metabarcoding pipeline](https://github.com/ ...@@ -8,7 +8,7 @@ OTU clustering based on [TARA Fred's metabarcoding pipeline](https://github.com/
* linux system * linux system
* [python3](https://www.python.org/) * [python3](https://www.python.org/)
* [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/) or [pip3](https://pip.pypa.io/en/stable/) * [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/)
## Installation via Conda ## Installation via Conda
...@@ -61,9 +61,14 @@ wget -c https://gitlab.mbb.univ-montp2.fr/edna/tutorial_metabarcoding_data/-/raw ...@@ -61,9 +61,14 @@ wget -c https://gitlab.mbb.univ-montp2.fr/edna/tutorial_metabarcoding_data/-/raw
Simply type the following command to process data (estimated time: 20 minutes) Simply type the following command to process data (estimated time: 20 minutes)
``` ```
bash main.sh bash main.sh config/config_tutorial.yaml 8
``` ```
* This will generate OTU occurences tables into [results/06_assignment/04_table](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/tree/master/results/06_assignment/04_table)
* The first argument [config/config_tutorial.yaml](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/blob/master/config/config_tutorial.yaml) contains mandatory parameters information
* The second argument **8** is the number of CPU cores you want to allow the system use to run the whole workflow
# To go further # To go further
Please check the [wiki](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home). Please check the [wiki](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_swarm/-/wikis/home).
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