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Wastewater SARS-CoV-2 variant analysis tutorial #3793

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Wastewater SARS-CoV-2 variant analysis tutorial #3793

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PlushZ
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@PlushZ PlushZ commented Dec 23, 2022 •
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This tutorial explains workflows for detection of SARS-CoV-2 variants by genomic analysis of wastewater samples

@PlushZ PlushZ requested a review from a team as a code owner December 23, 2022 17:17
hexylena
hexylena reviewed Jan 20, 2023
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Looks like a great start! (Btw some of the citations in your bibliography are missing DOIs or URLs, would you mind adding one or the other to them?)

topics/variant-analysis/tutorials/sars-cov-2-wastewater/tutorial.md
- for each workflow
- for each workflow, a short version consisting in running workflows and a long version (step-by-step)

{% include _includes/cyoa-choices.html option1="Amplicon Short" option2="Amplicon Long" option3="Metatranscriptomic Short" option4="Metatranscriptomic Long" default="AmpliconShort" %}
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Cool! Great to see more CYOA tutorials :)

@bebatut bebatut requested a review from a team as a code owner January 26, 2023 14:33
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bebatut commented Feb 20, 2023

I think I am done with my big edits there.
So it is ready for other reviews. @wm75?

@github-actions github-actions bot added the faqs label Feb 28, 2023
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wm75 commented Feb 28, 2023

Finally on it, but will need some time to finish.

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wm75 commented Mar 1, 2023

Ok, so I have obtained a bit more overview over this training and its connections to galaxyproject/iwc#154.
As commented there, I guess I would prefer a more modular design of the WF, and I think this could even improve the training here because it would allow you to turn it into an interesting mix of manual and automated steps.
You could have users perform initial read filtering and taxonomy exploration manually, then have them run the exisitng IWC variation workflow, and finally perform the wastewater-specific freyja and cojac steps manually again.
This way you'd automate/speed up the boring, known parts of the analysis and could put a focus on what makes wastewater analysis special.
What do you think @PlushZ @bebatut ?

@wm75 wm75 marked this pull request as draft March 24, 2023 10:25
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@PlushZ @bebatut @wm75 @hexylena