Include metagenomics mini-course

[jeffe107]

This pull request includes both the pipeline and the documentation.

[vdauwera]

Thanks for contributing this detailed metagenomics pipeline tutorial!

• Prerequisites changes requested: This tutorial uses a few points of syntax that are not covered in Hello Nextflow, so they should be documented explicitly. One is the use of a main.nf and workflow with take/main syntax; for that you can point to the "Workflows of workflows" Side Quest. The other that jumped out at me is the use of log.info for which it would be good to link to documentation.
• Formatting changes requested: We prefer to start all sentences on a new line, even within paragraphs; see https://github.com/nextflow-io/training/pull/612/files (I realized this wasn't documented yet, so I've added a blurb to the CONTRIBUTION.md doc).
• I have a few edit suggestions for language but it would be best to do that after you update the text to have all sentences start on new lines. This will make tracking changes much easier.
• I think we should add a !!! note box in the course description acknowledging that this is a community contribution, both to credit you appropriately as the author, and to set expectations regarding support and maintenance.
• At some point in the near future we're going to rework how the left-hand menu displays courses, because we need to group/collapse the 'science' courses together for readability. But I don't want to hold up this PR on that, we can use the current setup and do that once this is merged.

The two I've bolded are top priority in my opinion. For the "community contribution" box we need to think a little about what the language should be, but feel free to propose something based on how you'd like to be credited and we can edit from there.

[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.