Scientific Workflow Management Systems comparison

[Lisanna]

1. What is the topic of your lesson or lesson proposal?

A comparison among workflow management systems used in the scientific field. The same workflow example (in the field of bioinformatics and in particular biological sequences analysis) will be run by the trainees in three different systems: Galaxy, Snakemake and Nextflow.

3. Do you already have a draft of your lesson? You're welcome to share materials at any stage of development. If you already have drafted materials, please include a link.

Repository link: github.com/Lisanna/scientific-workflow-systems

Rendered materials link: lisanna.github.io/scientific-workflow-systems/

While these links redirect to the Carpentries version of the lesson, full materials from a workshop hosted at EMBL in January 2022 can be found at: git.embl.de/grp-bio-it-workshops/workflow-management-systems-comparison.

4. Do your materials conform to our Code of Conduct?

Yes.

6. Are your materials already on GitHub and do they use The Carpentries lesson template? (you can visit our lesson example to learn more about how to use our template).

Yes

9. If you answered "Yes" to both parts of question 4, would you like to transfer your repository to The Carpentries Incubator? You will have Admin access to the repository.

Yes

10. If you answered "Yes" to either question 5 or 6, list the GitHub handles for people who should have Maintain access to your lesson. If you don't know how to answer this question, don't worry! We can always add collaborators later.

@unode

[MCMaurer]

Thank you for submitting this lesson to The Carpentries Incubator, @Lisanna!

You should have received an invitation to join a Team of maintainers for the lesson, as part of the carpentries-incubator organisation on GitHub. After you have accepted that invitation, you should be able to initiate the transfer into carpentries-incubator, via the repository Settings. When that is done, I will make sure that you retain the appropriate level of access to the repository: you will be given full administrative rights, and the collaborators you listed above will be given “Maintain” privileges. I have also added @unode to the Team.

To keep in touch with The Carpentries curriculum community you may find it useful to join the incubator-developers list on The Carpentries TopicBox and/or the lesson-dev channel on The Carpentries Slack. Joining the Slack channel requires that you first become a member of that workspace.

I also wanted to point you towards several existing Incubator lessons on workflow software: a Nextflow lesson, a fairly active Snakemake lesson and a less active Snakemake lesson. Your lesson is certainly different enough from these existing lessons, but since it is (at least currently) more of a comparison than a full lesson on any of the three tools, it probably makes sense to think about how your lesson may interface with these others. For example, what would it look like to teach your lesson in a workshop setting vs. teach it jointly with another lesson? I think it is also worth emphasizing in the lesson title that the software and example workflows are geared towards a bioinformatics audience, just for the sake of clarity.

I will leave this issue open until the transfer has been completed. If you have any questions about the process, or if you run into any trouble, please post back here and I will be happy to help you.