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

add docs for bcftools annotate params #1335

Merged
merged 11 commits into from
Nov 20, 2023
Merged

add docs for bcftools annotate params #1335

merged 11 commits into from
Nov 20, 2023

Conversation

FriederikeHanssen
Copy link
Contributor

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).

@FriederikeHanssen
Copy link
Contributor Author

adding some validation as well...

@FriederikeHanssen FriederikeHanssen marked this pull request as draft November 16, 2023 10:28
@github-actions GitHub Actions
Copy link

github-actions bot commented Nov 16, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa45aab

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-20 07:46:30

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review November 16, 2023 10:34
@FriederikeHanssen
Copy link
Contributor Author

@nf-core-bot fix linting

@FriederikeHanssen
Copy link
Contributor Author

@nf-core-bot fix linting

maxulysse
maxulysse reviewed Nov 16, 2023
View reviewed changes
nextflow_schema.json Outdated Show resolved Hide resolved
@FriederikeHanssen
Copy link
Contributor Author

@nf-core-bot fix linting

@maxulysse
Copy link
Member

failing tests are just the sention ones, so ok to merge

@FriederikeHanssen FriederikeHanssen merged commit 7f114f7 into nf-core:dev Nov 20, 2023
22 of 27 checks passed
@FriederikeHanssen FriederikeHanssen deleted the fix_annotate_docs branch November 20, 2023 08:14
@maxulysse maxulysse mentioned this pull request Dec 8, 2023
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@grantn5 grantn5 grantn5 left review comments

@maxulysse maxulysse maxulysse 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.
4 participants
@FriederikeHanssen @maxulysse @grantn5 @nf-core-bot