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

Move all vep args from ext.args to params.vep_custom_args #1157

Merged
merged 2 commits into from
Jul 20, 2023
Merged

Move all vep args from ext.args to params.vep_custom_args #1157

merged 2 commits into from
Jul 20, 2023

Conversation

maxulysse
Copy link
Member

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/sarek 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).

@github-actions
Copy link

github-actions bot commented Jul 20, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅

Posted for pipeline commit 76120fd

+| ✅ 152 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-20 09:55:01

@asp8200
Copy link
Contributor

asp8200 commented Jul 20, 2023

That should work fine. Can you just remind me why you want to move the vep args from ext.args to params.vep_custom_args?

@maxulysse
Copy link
Member Author

That should work fine. Can you just remind me why you want to move the vep args from ext.args to params.vep_custom_args?

Because it's a mess to actually update any args in the ext.args.
So by moving all default args in the params, it'll be easier for users to just add or remove a single one.
Also I'm guessing we can actually work on the vcf output for VEP since it was vcf by default and without any way to change

@maxulysse maxulysse merged commit 967c248 into nf-core:dev Jul 20, 2023
25 checks passed
@maxulysse maxulysse deleted the vep_custom_args branch July 20, 2023 10:28
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@asp8200 asp8200 asp8200 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
@maxulysse @asp8200