Include metagenomics mini-course

[jeffe107]

This pull request includes both the pipeline and the documentation.

[jeffe107]

Hello,

Thank you for your comments. I already applied the main changes that you suggested in this PR. I included the !!!note at the very beggining of the course, please feel free to modify it and move it to he best location you consider suitable. I remain ready to apply further changes you consider necessary.

Best,

[vdauwera]

Thanks @jeffe107! I'm finishing up a couple of big chunks of work then I'll work on getting this over the finish line.

[vdauwera]

Hi @jeffe107, sorry it's taken me so long to get to this!

So far I've made only cosmetic/minor edits, mostly to deal with things our syntax checker was choking on. As part of that I had to edit the indentation of some of the code files and the report.Rmd file; the nf files I'm confident are fine but please do check that I haven't messed anything up in the Rmd file. I will also run through this to check that everything works in my hands but it would be good to have your expert eye on this as well.

The other thing I want to do is take another look at the headings of the various sections to see if we can maybe make them a bit more meaningful. I'm going to try to expedite this so we can get this merged without much further delay.

[jeffe107]

Hi @vdauwera,

Thank you for your support. I checked the pipeline execution, and it is working fine. I just fixed a typo that I spotted regarding the path to execute the single sample run. Further, for the title modifications, please feel free to adjust them to send a clear message, or let me know which ones specifically you would like to modify.

I remain ready if anything else is needed.

[vdauwera]

A few explanations of what has changed because the diff is not really helpful (sorry).

The structural change is fairly minor, I just split the single-sample implementation into its own file, separate from the description of the overall workflow design. So now Part 1 just has the method and workflow description, and Part 2 is the single-sample implementation walkthrough (like in the RNAseq course).

For the method overview and the single-sample parts, I've edited the text to break apart some of the bigger chunks of text, add subheadings, and generally clarify some of the explanations in line with our usual style.

The multi-sample implementation walkthrough is now Part 3; that's just been renamed, I haven't made any changes there yet. Will do some text editing next.

[vdauwera]

Btw not sure if this was obvious but you can see the rendered preview here: https://deploy-preview-577--nextflow-training.netlify.app/nf4_science/metagenomics