Commit efef592d authored by Midoux Cedric's avatar Midoux Cedric
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First update README.md

parent 4faf66b6
# workflow_metagenomics
# Workflow Metagenomics
This pipeline is currently adapted for use on the [INRAE MIGALE](https://migale.inrae.fr/) cluster.
## Settings
In this folder, in a parent folder `../my_project` :
* Place the raw data in the folder `DATA/raw/` (or `../my_project/DATA/raw/`).
* Edit the file [`config.json`](config.json)
* Adapt the file [`cluster.json`](cluster.json)
* Select the desired outputs in the file [`global.smk`](global.smk)
## Running
For simple use :
```bash
./RunSnake.sh global.smk
```
For a dry-run :
```bash
./RunSnake_printshellcmds.sh global.smk
```
For a SGE submission :
```bash
./qsubSnake.sh global.smk
```
For a jobs visualisation :
```bash
./RunSnake_graph.sh global.smk
```
## Results
All results are available :
* In the folder `work/` for intermediate results,
* In the folder `report/` for reports.
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