diff --git a/README.md b/README.md index 9feebbd856e0db8b6cf593b1065207b048c65322..5444641672fac03fdde786727fb67e0a381c67e4 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,45 @@ -# 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.