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

Split vep_cache into vep_cache and vep_plugin_files #314

Merged
merged 3 commits into from
Aug 15, 2024
Merged

Split vep_cache into vep_cache and vep_plugin_files #314

merged 3 commits into from
Aug 15, 2024

Conversation

fellen31
Copy link
Collaborator

@fellen31 fellen31 commented Aug 13, 2024 •
edited
Loading

This PR takes a slightly different approach than raredisease and tomte, and makes --vep_plugin_files a mandatory parameter when annotating SNVs, it also separates the VEP cache input from the VEP plugins input completely.

The reason for this is that many clusters already provide a copy of the VEP cache (without plugins), in locations without write permissions. And it feels reasonable to provide all plugin file with one vep_plugin_files instead of some with vep_cache and some with vep_plugin_files. More on this: nf-core/raredisease#594 (review)

For the tests to pass this requires updating the test data files, I will wait to do so until the other open PRs have been merged.

Closes #259.

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
  • 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 Aug 13, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅

Posted for pipeline commit 6d22388

+| ✅ 160 tests passed       |+
#| ❔  17 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nallo_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nallo_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-14 15:50:21

@fellen31 fellen31 force-pushed the vep_extra_files branch 2 times, most recently from 3388c21 to fa34748 Compare August 13, 2024 17:28
@fellen31 fellen31 mentioned this pull request Aug 14, 2024
Merged
12 tasks
@fellen31 fellen31 marked this pull request as ready for review August 14, 2024 11:26
@fellen31 fellen31 requested a review from a team as a code owner August 14, 2024 11:26
@fellen31 fellen31 mentioned this pull request Aug 14, 2024
Merged
10 tasks
jemten
jemten reviewed Aug 14, 2024
View reviewed changes
Copy link
Collaborator

@jemten jemten 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, a couple of small comments

conf/modules/snv_annotation.config Outdated Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
workflows/nallo.nf Outdated Show resolved Hide resolved
@fellen31 fellen31 force-pushed the vep_extra_files branch 3 times, most recently from b4abee2 to 6d22388 Compare August 14, 2024 15:48
@fellen31
Copy link
Collaborator Author

Should be fixed!

jemten
jemten approved these changes Aug 15, 2024
View reviewed changes
Copy link
Collaborator

@jemten jemten left a comment

Choose a reason for hiding this comment

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

👍

@fellen31 fellen31 merged commit 341b8b5 into genomic-medicine-sweden:dev Aug 15, 2024
14 checks passed
@fellen31 fellen31 deleted the vep_extra_files branch August 15, 2024 13:06
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jemten jemten jemten approved these changes

Assignees
No one assigned
Labels
None yet
Projects
Nallo
Archived in project
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Use vep_plugins instead of putting plugins in cache
2 participants
@fellen31 @jemten