workflow

A WORKFLOW-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-run-workflow

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

A set of output files generated by anvi-run-workflow for a given anvi’o workflow. An anvi’o workflow is a set of instructions to be run via Snakemake.

As of now, the available workflows include,

• Contigs workflow
• Metagenomics workflow
• Pangenomics workflow
• Phylogenomics workflow
• tRNAseq workflow
• EcoPhylo workflow
• SRA-download workflow

Each workflow writes logs into 00_LOGS, with one subdirectory per workflow or named run. Rule logs are organized by rule name, as in 00_LOGS/metagenomics/anvi_profile/G01-S01.log or 00_LOGS/sra_download/check_md5sum/SRR5965623.log.

Workflow runs also write a tab-delimited manifest named <workflow-name>-workflow-manifest.tsv in the workflow-specific log directory, such as 00_LOGS/metagenomics/metagenomics-workflow-manifest.tsv. The manifest reports each Snakemake job’s status, rule name, group and read wildcards when available, the rule log path, and the Snakemake log path when Snakemake reports one.

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