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Add reference recommendations to usage docs

Open lazappi opened this issue 1 year ago • 5 comments

Adds a section to the usage docs providing more information and recommendations about reference files. Fixes #1086.

PR checklist

  • [x] 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 you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • [ ] If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
  • [ ] Make sure your code lints (nf-core lint).
  • [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • [ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • [x] Usage Documentation in docs/usage.md is updated.
  • [ ] Output Documentation in docs/output.md is updated.
  • [ ] CHANGELOG.md is updated.
  • [ ] README.md is updated (including new tool citations and authors/contributors).

lazappi avatar Jun 11 '24 08:06 lazappi

I've opened this a draft as I think it would be good to get more comments etc. before merging. Most of the checklist didn't seem relevant for a docs only change and I wasn't sure how to edit CHANGELOG.md.

lazappi avatar Jun 11 '24 08:06 lazappi

Good suggestions on content, but much of this is already covered, if at a lower level of detail, in the pre-existing material.

I've suggested some minor improvements to flow etc of your additions, but in general these need to be worked into existing sections to make sure we're not repeating ourselves.

This was just a bit of an information dump to start with but I agree it makes sense to combine with what is already there. I guess I overlooked it because it is an "options" section further down and I figured that was more about the technical details of the different arguments and not so much the broader question of which genome/annotation to use. Could we move the combined section closer to the start as it's likely to be relevant to more users than the options sections?

lazappi avatar Jun 12 '24 06:06 lazappi

Good suggestions on content, but much of this is already covered, if at a lower level of detail, in the pre-existing material. I've suggested some minor improvements to flow etc of your additions, but in general these need to be worked into existing sections to make sure we're not repeating ourselves.

This was just a bit of an information dump to start with but I agree it makes sense to combine with what is already there. I guess I overlooked it because it is an "options" section further down and I figured that was more about the technical details of the different arguments and not so much the broader question of which genome/annotation to use. Could we move the combined section closer to the start as it's likely to be relevant to more users than the options sections?

Let's postpone reorganisation for a future PR (@drpatelh may have views), and stick with the new content integration for the moment.

pinin4fjords avatar Jun 12 '24 08:06 pinin4fjords

@pinin4fjords I've incorporated your suggestions and moved the new content to the existing sections

lazappi avatar Jun 14 '24 10:06 lazappi

Thanks alot for this @lazappi ! We will include it in the next release!

Would love for @tdanhorn @MatthiasZepper to give this a once over too since they were involved in discussions in the parent issue.

PS: I also sent you an invite to become a member of the nf-core community on Github. Hopefully, future contributions won't have to be approved on PRs.

drpatelh avatar Jun 21 '24 10:06 drpatelh

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit c016418

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-15 09:42:34

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