A biobakery workflow pipeline for Whole Metagenome Shotgun (wmgx) data processing implemented using Snakemake rather than AnADAMA2. Programs supported thus far are Kneaddata, Metaphlan, and Humann2.
https://bitbucket.org/biobakery/biobakery_workflows/wiki/Home
Intended to run for example data in the example-data directory. If real data is to be used, some changes are necessary.
To run on HPC cluster:
$ sh run_biobakery_workflow.sh
To run locally (for testing purposes) WARNING computational heavy :
$ /shares/hii/sw/snakemake/latest/bin/snakemake
Singularity Image can be found at:
$ /shares/hii/images/morenoj/biobakery