[New Tutorial] Taxonomic Analysis of eDNA

[jbeli11]

I have written a tutorial for the taxonomic analysis of environmental DNA sequences as part of my master's degree thesis and have added myself as a contributor to be able to submit it for review for approval.

[shiltemann]

Thanks a lot for your conributing @jbeli11!

Just some tiny initial comments about the folder structure:

please remove slashes from your folder names, they are interpreted as subfolders. All your tutorial files should be in a folder like topics/sequence-analysis/tutorials/eDNA-taxonomic-analysis/

with inside here directly the tutorial.md file and the workflows and images folder

I can also do this for you if you like, just let me know!

[jbeli11]

please remove slashes from your folder names, they are interpreted as subfolders. All your tutorial files should be in a folder like topics/sequence-analysis/tutorials/eDNA-taxonomic-analysis/

with inside here directly the tutorial.md file and the workflows and images folder

Is this something that can be done within the github interface or would it require reorganizing the folders locally and then reuploading them?
I apologize if this is a basic question, I'm still rather new to using github.

Thank you for your help with this!

[shiltemann]

@jbeli11 I am not sure if it can be done via the interface to be honest, but I can do it from the commandline for you, since it doesnt make sense to re-upload in my opinion.

[shiltemann]

ok, I pushed some changes to apply the re-organisation, depending on how you are using git you may have to do a git pull to see them where you are making changes.

Let me know if you run into any issues with this, or have any other git questions, it can be a bit of a learning curve if you're new to GitHub and that's totally ok!

[jbeli11]

do you know how to resolve the following error:
For the Links > Internal check, the following failures were found:

• At ./_site/training-material/topics/sequence-analysis/tutorials/eDNA-taxonomic-analysis/tutorial.html:494:

  internally linking to /training-material/hall-of-fame/jbeli11/, which does not exist

HTML-Proofer found 1 failure!
Error: Process completed with exit code 1.

[shiltemann]

@jbeli11 I think it's just a typo, seems that you used two l's in the CONTRIBUTORS.yaml file (jbelli11 instead of jbeli11), if you fix it in that file the error should go away :)

[shiltemann]

Thanks again @jbeli11!

A couple more minor suggestions from the GTN technical side below. You should be able to just hit the "commit suggestion" button on my comments to automatically apply them (if you agree with them of course)

A general question: have you been able to get a live preview of your tutorial? If not, please have a look at this tutorial to get a preview using CodeSpaces (all online, no installation required)

[jbeli11]

Thank you for the valuable input @shiltemann !
I have applied your suggestions. I have been viewing the preview from the github branch folder but I'll switch gears to start viewing from CodeSpaces

[jbeli11]

Would the issues causing the linting to fail be related to the tutorial.md as well or something else that needs troubleshooting?

[yvanlebras]

Hi John! THANK you for this new training material! Considering the eDNA topic, it can be of interest 1/ to propose this tutorial in the ecology topics 2/ to look at the existing tutorial https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/tutorial.html maybe to write some line about similarities and/or differences (and the same can be done on the Obitools tutorial). Please, don't hesitate to say if this can be relevant or not and if I can help somewhere ! I can at least try your tutorial and maybe review it!

[shiltemann]

@yvanlebras thanks! I agree it would be nice to move this into the ecology topic, and if you can test the tutorial and review it that would be great!

@jbeli11 I will look into the error, might be unrelated to your changes.

[shiltemann]

@jbeli11 the linting error came from the data-library.yaml file, so I let our automations re-create it from the Zenodo link. I also moved your tutorial into the ecology topic.

@yvanlebras please advise on the best ecology subtopic for this tutorial, and review the scientific content.

From a technical perspective this looks good :)

[yvanlebras]

Nice and clear tutorial! Thank you!

It is eDNA oriented due to input datasets but in fact it shawos how to use classical tools to look at taxonomic informzations from raw sequencing data.

For a specific comment, maybe it is better to change Count (last tool) How should the results be sorted? * parameter so it is easier to look at results and evaluate directly the most common sequence identified.

I made a mistake, wanted to propose some modifications, but made it through a direct commit.. Sorry, don't hesitate to change it!