anvi-run-workflow [program]

Execute, manage, parallelize, and troubleshoot entire 'omics workflows and chain together anvi'o and third party programs.

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Alon Shaiber
Matthew Schechter

Can consume

samples-txt fasta-txt workflow-config

Can provide

contigs-workflow metagenomics-workflow pangenomics-workflow phylogenomics-workflow trnaseq-workflow


This program allows you to run Snakemake workflows for common anvi’o processes. It is described fully in this tutorial.

Essentially, an anvi’o workflow will run several anvi’o programs for you in quick succession (based on a standard set of intiial steps that will allow you to quickly get to a point where you can ask novel questions).

As of now, the available workflows are the contigs-workflow, the metagenomics-workflow, the pangenomics-workflow, the phylogenomics-workflow, and the trnaseq-workflow.

Before running the workflow

Each workflow requires a workflow-config: the file that details all of the parameters for the workflow. To get the workflow-config with the default parameters, just run

anvi-run-workflow -w WORKFLOW-NAME \ --get-default-config CONFIG.json

Before running a workflow, it is also a good idea to check the required dependencies by running

anvi-run-workflow -w WORKFLOW-NAME \ --list-dependencies

The main run

The main run of the workflow should look like this:

anvi-run-workflow -w WORKFLOW-NAME \ -c CONFIG.json --save-workflow-graph

The flag --save-workflow-graph creates a visual representation of the anvio programs that the workflow you’re running used.

You can also use the -A flag at the end of the parameter list to change other Snakemake parameters.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.