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

Try fixing antismash and prokka incompatibility #205

Merged
merged 10 commits into from
Feb 1, 2023
Merged

Try fixing antismash and prokka incompatibility #205

merged 10 commits into from
Feb 1, 2023

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Jan 30, 2023

AS discussed in gather.town

Ensures that the input FASTA file has the same head names as in the GFF file, by using the annotation output's FNA rather than our raw 'non-renamed' input FASTA, to ensure FNA + GFF name entries are the same

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/funcscan 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 requested review from jasmezz and louperelo January 30, 2023 14:31
@github-actions
Copy link

github-actions bot commented Jan 30, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a558349

+| ✅ 157 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_description - No description provided in schema for parameter: annotation_prokka_centre

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-01-31 14:55:17

jfy133
jfy133 commented Jan 30, 2023
View reviewed changes
jfy133
jfy133 commented Jan 30, 2023
View reviewed changes
jfy133
jfy133 commented Jan 30, 2023
View reviewed changes
louperelo
louperelo approved these changes Feb 1, 2023
View reviewed changes
Copy link
Contributor

@louperelo louperelo 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 jfy133 merged commit 96a5334 into dev Feb 1, 2023
@jfy133 jfy133 deleted the prokka-antismash-fix branch February 1, 2023 09:51
@github-actions
Copy link

github-actions bot commented Feb 1, 2023

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@louperelo louperelo louperelo approved these changes

@jasmezz jasmezz Awaiting requested review from jasmezz

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

Successfully merging this pull request may close these issues.
3 participants
@jfy133 @louperelo @jasmezz