Workflow Metagenomics

This pipeline is currently adapted for use on the INRAE MIGALE 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
• Adapt the file cluster.json
• Select the desired outputs in the file global.smk

Running

For simple use :

./RunSnake.sh global.smk

For a dry-run :

./RunSnake_printshellcmds.sh global.smk

For a SGE submission :

./qsubSnake.sh global.smk

For a jobs visualisation :

./RunSnake_graph.sh global.smk

Results

All results are available :

• In the folder work/ for intermediate results,
• In the folder report/ for reports.