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

allow vep 112 #617

Merged
merged 4 commits into from
Sep 26, 2024
Merged

allow vep 112 #617

merged 4 commits into from
Sep 26, 2024
+5 −4

Conversation

jemten
Copy link
Collaborator

@jemten jemten commented Sep 24, 2024 •
edited
Loading

PR checklist

The vep module uses version 112, yet the pipeline does not allow the cache to be set to that version

  • 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>).
  • 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).

Sorry, something went wrong.

@jemten
allow vep 112

Verified

This commit was signed with the committer’s verified signature.
legendecas Chengzhong Wu
GPG key ID: CB3C9EC2BC27057C
Verified
Learn about vigilant mode
Loading
Loading status checks…
2a505df
@github-actions GitHub Actions
Copy link

github-actions bot commented Sep 24, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e583e15

+| ✅ 187 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • 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
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-25 20:10:14

@jemten
prettier
Loading
Loading status checks…
1021df2
ramprasadn
ramprasadn reviewed Sep 24, 2024
View reviewed changes
nextflow_schema.json Outdated
"description": "Specify the version of the VEP cache provided to the `--vep_cache` option.",
"fa_icon": "fas fa-align-center",
"enum": [107, 110]
"enum": [107, 110, 112]
Copy link
Collaborator

Choose a reason for hiding this comment

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

Should we allow 111 as well?

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

Kind of thinking we should remove this enum altogether and just have the requirement on it being a number.

Copy link
Collaborator

Choose a reason for hiding this comment

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

Yeah, that's better actually 😅

@ramprasadn ramprasadn merged commit 985230b into dev Sep 26, 2024
6 checks passed
@ramprasadn ramprasadn deleted the add_vep_112_option branch October 1, 2024 14:19
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ramprasadn ramprasadn

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

Successfully merging this pull request may close these issues.

None yet
2 participants
@jemten @ramprasadn