Two Tutorials Added: Simulating Illumina Reads and Uploading Data to Cavatica

[abhijna]

PR Checklist

• Release label added
• PR category label added
• PR mergeable
• Clean build logs
• Linked related issues
• Colorblindness test https://www.toptal.com/designers/colorfilter/

PR Description

This is a new tutorial about using InSilicoSeq to simulating fastq data from a user-specified version of the human reference genome. It also includes some QC steps to see how the simulation looks. While this tutorial is good for simulating fastq reads from normal human samples, it cannot simulate mutations or indels.

Need someone to run through everything and make sure 1) that 16GB is enough for it all. 2) that it all works. I haven't done the formatting yet. If there are things you notice and can change easily, please do. If not, leave me a comment and I can fix it when I get to it.

Also added the command line uploader tutorial here. Was going to make a new PR but I pushed changes to this branch by mistake. Sorry :(
Same deal for this tutorial as well. Check if everything run, look for typos, formatting problems, other ways to improve it.

Preview link
https://cfde-training-and-engagement--263.com.readthedocs.build/en/263/Bioinformatics-Skills/Simulate_Illumina_Reads/

Review format

Direct editing or comments are ok.

Timeline

This is due for December release. Don't care when you give me detailed comments as long as you give me enough time to incorporate your changes. If you can run through the code and let me know if it all installs on your computer in the next two weeks, that would be helpful.

[abhijna]

I made all the changes. Put two of the comments (about md5sum and screencasts) into issues for the next release.

[jeremywalter]

RE: minor edits commit -- I already did that? could create a conflict? leaving this here for reference in case it does (how did that happen?)

[marisalim]

@abhijna for the Cavatica uploader tutorial:

• all the steps worked!
• minor: the cavatica uploader is a ".tgz" file, but the explanation of the tar command talks about "tar.gz" extension. are they the same? ---> yes it is the same. I changed it to say .tgz :)
• this can be an edit for next iteration, but i think it would be best to stick to 1 example dataset - show the yeast example files in the Cavatica screenshots instead of the sim data ones. ---> yeah, i'd have to redo all the screenshots. so this can be a thing for next time.
• add a note/link to close down the AWS instance at the end of the tutorial. ---> done

[abhijna]

Done :)

[marisalim]

looks like all the changes i requested got added! good to go