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Docs and tutorials updates#491

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apeltzer merged 48 commits intodevfrom
docs-updates
Jul 15, 2020
Merged

Docs and tutorials updates#491
apeltzer merged 48 commits intodevfrom
docs-updates

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@jfy133
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@jfy133 jfy133 commented Jul 7, 2020

nf-core/eager pull request

Many thanks for contributing to nf-core/eager!

Please fill in the appropriate checklist below (delete whatever is not relevant).
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  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
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  • Documentation in docs is updated
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@jfy133 jfy133 marked this pull request as draft July 7, 2020 12:58
@jfy133 jfy133 changed the title Docs updates Docs and tutorials updates Jul 7, 2020
@apeltzer apeltzer merged commit 7cccd05 into dev Jul 15, 2020
@apeltzer apeltzer deleted the docs-updates branch July 15, 2020 06:45
@ewels
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ewels commented Jul 15, 2020

@jfy133 - the tutorial about config profiles is great! But it's not specific to the eager pipeline really. What do you think above moving it to the website, maybe at https://nf-co.re/usage/configuration ? Would be great to have it available for the whole @nf-core community!

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jfy133 commented Jul 15, 2020

Thanks @ewels - I was actually trying to put it quietly on EAGER and get some feedback from the aDNA field first. However of course you're right.

That said I actually just took a stab at combining the two but I'm not finding what I've already written really meshes well with the configuration page, which is already very well written but is sort of talking about a different thing. The way I've written the tutorial is very much like an actual tutorial, and also focuses on the whole institutioanl profile thing rather than profiles for pipeline-specific parameters. I almost feel it would make more sense to have a 'tutorials' section on a webpage, becuse at least what i've written is trying to aim more towards every-day users of the pipeline rather than bioinformaticians with knowledge how clusters/schedulers etc works.

I will keep what I've written already in eager first, but then open an issue and we can discuss it.

@ewels
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ewels commented Jul 15, 2020

Ah sorry, you can blame @apeltzer for letting the cat out of the bag 😅

More and smaller / more specific tutorials for the website would be great 👍 Same logic applies as docs though I think, would be good to keep the more general stuff in a central location rather than tied to pipelines (when you're ready of course!).

The fact that the config page is talking about a different thing is kind of why I thought this would be a good addition. I'm not sure that we really describe profiles as well as this anywhere..

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Sorry, probably was too excited already 😅

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Add output docs for all non-default modules. Unclear output doc figure for Samtools flagstat and add MALT/KRAKEN/MVA etc.

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