🐍 ⬆️ Add snakemake workflow file

[Sidduppal]

• Add snakemake workflow file for Autometa
• Add config file to submit the workflow on slurm

Command to run (user should be in the directory where the snakefile is or point to it). The simple directory has the config to submit the jobs on slurm:

snakemake --profile simple/

PR checklist

• [X] This comment contains a description of changes (with reason).
• [X] Have you followed the pipeline conventions in the contribution docs

[chasemc]

I don't have a deciding opinion here, but would suggest limiting the addition of additional workflow managers

I’m not sure where the responsibility lies for long-term maintenance but there’s currently a Nextflow pipeline, a Bash script pipeline, and the python code itself. That’s already a large amount of maintenance liability and will require redundant changes to each of the different workflow managers (and expertise in each of those) to make any additions/modifications to the overall workflow.

Would suggest roping @jason-c-kwan if the ultimate maintenance responsibility is on the lab itself

[evanroyrees]

Some resources for PR review:

• snakemake readthedocs
• snakemake best practices
• Integrating Foreign Workflow management systems, i.e. use of existing autometa.nf?
• Equivalent report similar to report written by nextflow?
• Equivalent GUI for end-users?

[evanroyrees]

Some Pros & Cons for consideration

👎 ~It would be nice if snakemake had an nf-core equivalent to automatically generate a GUI for the end-user. At the moment, I'm unaware of a similar tool~ 👍 The snakemake framework is written in python, so the overhead of having to learn an additional language and two frameworks is no longer necessary (i.e. groovy, nextflow, nf-core) 👍 snakemake generates its own unit tests.. I have not tried this before, but what a nice feature this would be if it works as suggested. See snakemake --generate-unit-tests

Hopefully others have some thoughts as well 🧠 ⚡

Did some searching...

👎 ➡️ 👍 snakemake has a GUI ready to go, no additional framework needed. See cli options snakemake --gui 👍 Alot of nice utilities that could be used to help further describe the Autometa workflow. See utilities docs

[evanroyrees]

Closing. If interested in trying snakemake with Autometa, please see @Sidduppal gists