anvi-run-workflow

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

🔙 To the main page of anvi’o programs and artifacts.

Authors

Requires

workflow-config

Provides

workflow

Usage

This program allows you to run a workflow implemented by anvi’o developers for various commonly used set of steps to typically process your raw data (i.e., short reads or contigs from genomes, transcriptomes, metagenomes, metatranscriptomes, etc). Some aspects of this program is described in this tutorial.

For a list of currently available anvi’o workflows, please see the workflow artifact.

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

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

The main run

The main run of the workflow should look like this:

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.

Logs and the workflow manifest

Every workflow run writes rule logs under 00_LOGS, within a subdirectory for the workflow or named run. Logs are then organized by rule name:

For instance, a metagenomics profiling job may write to 00_LOGS/metagenomics/anvi_profile/G01-S01.log, while an SRA download checksum job may write to 00_LOGS/sra_download/check_md5sum/SRR5965623.log.

Each workflow run also creates a tab-delimited manifest in the same workflow-specific log directory:

This file lists the status of each Snakemake job, the rule name, the group and read wildcards when they exist, the rule log path, and the Snakemake log path when Snakemake reports one. If a workflow stops because a rule failed, this manifest is often the quickest way to find the relevant rule log.

Edit this file to update this information.

Additional Resources

• Tutorial

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.