snakemake rules for running anvio
This Snakefile will run a basic anvi'o analysis of a set of assemblies and a set of samples, using the snakemake workflow manager.
The file containing the snakemake rules
An example file containing the specific sample and assembly names that will be used in the workflow, as well as additional variable specifications.
Must be renamed 'config.yaml' for use.
A file specifying compute cluster job resource parameters for particular rules in the Snakefile.
A file specifying conda requirements for the snakefile conda environment
Example launch command for launching on a Torque (qsub) job manager
The commands I used for setting up my Anvi'o conda environment on Centos6
Visualization of the workflow steps run when executing the example config.yaml
Fake example data structure. For your own data, replace the files in data/assemblies and data/samples with the assembled contigs and the per-sample paired-end gzipped fastqs, respectively. Files must be named [assembly].fa and [sample].R[1,2].fq.gz