Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Standardised taxon table and mOTU database docs improvement #271

Merged
merged 2 commits into from
Mar 21, 2023
Merged

Standardised taxon table and mOTU database docs improvement #271

merged 2 commits into from
Mar 21, 2023

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Mar 17, 2023

Closes #267

PR checklist

  • 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/taxprofiler 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>).
  • 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).

@jfy133 jfy133 linked an issue Mar 17, 2023 that may be closed by this pull request
Unclear points in documentation #267
Closed
@github-actions
Copy link

github-actions bot commented Mar 17, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e0b112c

+| ✅ 156 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_lint - Schema 'description' should be 'Taxonomic classification and profiling of shotgun metagenomic data'
    Found: 'Taxonomic profiling of shotgun metagenomic data'

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-21 07:46:50

@sofstam sofstam self-requested a review March 20, 2023 13:48
sofstam
sofstam approved these changes Mar 20, 2023
View reviewed changes
Copy link
Collaborator

@sofstam sofstam left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Lgtm!

@jfy133
Copy link
Member Author

jfy133 commented Mar 20, 2023

@prototaxites does this cover everything for you?

@prototaxites
Copy link

Yes, this clears things up well from my perspective as a user!

@sofstam sofstam merged commit 5879526 into dev Mar 21, 2023
@sofstam sofstam deleted the prototaxites-docs-updates branch March 21, 2023 09:14
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@sofstam sofstam sofstam approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Unclear points in documentation
3 participants
@jfy133 @prototaxites @sofstam