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

Re-add unused GTDBTK parameters #671

Merged
merged 8 commits into from
Sep 23, 2024
Merged

Re-add unused GTDBTK parameters #671

merged 8 commits into from
Sep 23, 2024

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Sep 18, 2024

Closes #670

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/mag 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>).
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Sep 18, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c57286b

+| ✅ 306 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-23 18:33:35

harper357
harper357 requested changes Sep 18, 2024
View reviewed changes
nextflow.config Outdated Show resolved Hide resolved
subworkflows/local/gtdbtk.nf Outdated Show resolved Hide resolved
CHANGELOG.md Outdated Show resolved Hide resolved
harper357
harper357 approved these changes Sep 20, 2024
View reviewed changes
Copy link
Contributor

@harper357 harper357 left a comment

Choose a reason for hiding this comment

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

Looks good to me

@jfy133
Copy link
Member Author

jfy133 commented Sep 23, 2024

Thanks @harper357 !

@jfy133 jfy133 merged commit 32298dd into dev Sep 23, 2024
15 checks passed
@jfy133 jfy133 deleted the gtdbtk-missing-params branch September 23, 2024 18:24
@jfy133 jfy133 mentioned this pull request Sep 23, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@harper357 harper357 harper357 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.
2 participants
@jfy133 @harper357