[Review]: metagenomics

[nselem]

Thank you for your interest in submitting your lesson for review in The Carpentries Lab! Please respond to the prompts below to complete your submission. Check boxes by adding an 'x' between the square brackets at the start of each point, or submit the issue and check off the boxes afterwards.

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1. What is the title of the lesson? Metagenomics Workshop Overview

2. Provide URLs to

   • The lesson repository: https://github.com/carpentries-incubator/metagenomics-workshop

   • The lesson homepage: https://carpentries-incubator.github.io/metagenomics-workshop/

3. Briefly describe the lesson (50 words or fewer). What does it aim to teach and to whom? This workshop teaches data management and analysis for metagenomics research, including best practices for organizing bioinformatics projects and data and connecting to and using cloud computing. It also provides experience using command-line utilities and tools to analyze sequence quality and R studio and R libraries to compare diversity between samples.

4. If you are submitting this lesson for review on behalf of multiple authors, list the GitHub usernames below for all authors who should receive notifications relating to the review. AbrahamAvelar, aaronejaime, fabel134, Vanessaarfer, Czirion, Bedxxe, nselem, BwanyaBrian, EdderDaniel, ahmedmoustafa

5. Provide URLs to workshop webpages and/or an issue on the lesson repository from any beta pilots of the lesson. (A beta pilot is a workshop where the lesson was taught by any instructor who was not part of the lesson development team before the pilot took place.) Alpha workshop https://betterlabmx.github.io/2020-11-27-BetterLab/ First beta pilot https://czirion.github.io/2021-06-30-BetterLab-online/ The second beta pilot was a course in a University, Here we provide the letter of the University to the professor: Guanajuato University Letter

6. (Optional) If you have obtained a DOI for the lesson via Zenodo, paste that DOI below. 10.5281/zenodo.4285901

7. If the lesson is similar in topic to any other lesson already included in The Carpentries Lab and/or The Carpentries Lesson Programs (Software, Library, and Data Carpentry), briefly describe how this lesson differs and why a separate lesson was developed. This workshop is a curriculum that comprises four lessons. The first two lessons are adapted to metagenomics from the Genomics’ Data Carpentry. The third part includes a brief introduction to R, and the fourth lesson teaches a complete shotgun metagenomics workflow using public data which was not previously included in The Carpentrie’s lessons but it is a topic of interest to the biological community.

8. Check the boxes to confirm that the lesson

   • [x] is the the original work of the author(s), or that any content derived from another source is reused with permission and appropriate attribution.
   • [x] aligns with The Carpentries Code of Conduct.
   • [x] is published under a CC-BY or CC0 license.
   • [x] uses The Carpentries lesson template without significant customisation/adaptation.

9. If you wish to submit the lesson for publication in the Journal of Open Source Education (JOSE): (see the repository README for more details):

   • [x] check the box to confirm that your repository includes paper.md and paper.bib files as described in the JOSE submission guide for learning modules.

[tobyhodges]

Thank you @PaulaNietoG and @fpsom, this is very exciting. I know it takes considerable time to conduct a review on a whole curriculum like this, and I really appreciate the thorough and thoughtful approach you have both taken to it. I will follow up with you separately to request some feedback on your experience as reviewers.

@nselem @AbrahamAvelar, @aaronejaime, @fabel134, @Vanessaarfer, @Czirion, @Bedxxe, @nselem, @EdderDaniel, @bwanya, and @ahmedmoustafa I am delighted to be able to mark the curriculum as approved now. There are a few other steps to take, to transfer the curriculum into The Carpentries Lab and pass on the submission to JOSE. I am traveling today so may not get through everything before the weekend, in which case I will come back to the task at the start of next week.

[nselem]

Dear @tobyhodges, @PaulaNietoG and @fpsom, thank you for your time and effort that helped us improve the lesson. It has been an enriching experience for the team. @fpsom We hope that soon you can teach the lesson, we will be very happy.

[tobyhodges]

The lesson repositories have now all all been transferred into The Carpentries Lab. Here are the new repository locations:

• https://github.com/carpentries-lab/metagenomics-analysis/
• https://github.com/carpentries-lab/metagenomics-R/
• https://github.com/carpentries-lab/metagenomics-organization/
• https://github.com/carpentries-lab/metagenomics-workshop/
• https://github.com/carpentries-lab/metagenomics-shell/

Note that some of the repository names have changed, as well as their GitHub organisation. Those of you with local clones of these repositories should update your remotes accordingly (use git remote set-url for this).

I also renamed the default branch of metagenomics-organization to main, and anyone working with a local clone of that repository should run the following commands while working on their local master branch:

git branch rename master main
git push -u origin main

Finally, I recommend that you now publish a new release of each lesson repository to Zenodo.

[nselem]

By publishing the lesson, do you mean uploading all the local repositories to Zenodo? or just the data? If the answer is the repositories, should be one upload for all the five repositories, or separate uploads for each one?

[Czirion]

I was checking the new websites and it is so exciting to see "This lesson has passed peer-review!" in the lessons! Thank you so much. I just realized that this link https://carpentries-lab.github.io/metagenomics-organization/ for the Organization lesson is not working, and I couldn't find an error.

[tobyhodges]

Good catch, @Czirion, thanks. That was an unanticipated side effect of renaming the default branch - GitHub Pages was deactivated. It should be back up now.

[tobyhodges]

By publishing the lesson, do you mean uploading all the local repositories to Zenodo? or just the data? If the answer is the repositories, should be one upload for all the five repositories, or separate uploads for each one?

At the moment, I think only the data for the curriculum is published on Zenodo. So far, I have set that DOI to be linked from the banner at the top if each lesson site. However, I recommend that you now create a Zenodo entry for each lesson as well, which you can populate with a list of authors, maintainers, reviewers, etc. When those have been made, the _config.yml file can be updated in each repository with the relevant DOI information. This will make it easier for people to cite your lessons, and in future you can update the Zenodo entry with new releases of each lesson when you think those are necessary.

If and when the curriculum is accepted to JOSE, we can update the DOIs in the _config.yml files again, to point to the publication.

[tobyhodges]

Since the curriculum was accepted to JOSE yesterday, I am going to close this issue.

Congratulations again to all the reviewers, and thanks one more time to @fpsom and @PaulaNietoG for reviewing 🙌

[fpsom]

Well done, congratulations! :)