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

Subworkflow for mobile element annotation #483

Merged
merged 7 commits into from
Jan 19, 2024
Merged

Subworkflow for mobile element annotation #483

merged 7 commits into from
Jan 19, 2024

Conversation

jemten
Copy link
Collaborator

@jemten jemten commented Jan 18, 2024 •
edited
Loading

This PR adds the option to annotate the mobile elements with SVDB and VEP

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Jan 18, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d14976b

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-19 10:29:46

@jemten jemten marked this pull request as ready for review January 18, 2024 13:44
@jemten jemten requested a review from ramprasadn January 19, 2024 09:55
Lucpen
Lucpen reviewed Jan 19, 2024
View reviewed changes
Copy link
Contributor

@Lucpen Lucpen left a comment

Choose a reason for hiding this comment

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

Only very very minor comments :)

@jemten @Lucpen
Apply suggestions from code review
d14976b 
Co-authored-by: Lucía Peña-Pérez <lucia.pena.perez@scilifelab.se>
Lucpen
Lucpen approved these changes Jan 19, 2024
View reviewed changes
Copy link
Contributor

@Lucpen Lucpen left a comment

Choose a reason for hiding this comment

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

LGTM!

@jemten jemten merged commit d36de29 into nf-core:dev Jan 19, 2024
8 checks passed
@jemten jemten deleted the me_anno branch January 19, 2024 14:04
This was referenced Jan 19, 2024
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@Lucpen Lucpen Lucpen approved these changes

@ramprasadn ramprasadn Awaiting requested review from ramprasadn

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
@jemten @Lucpen