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

Ngscheckmate fix #1381

Merged
merged 2 commits into from
Jan 25, 2024
Merged

Ngscheckmate fix #1381

merged 2 commits into from
Jan 25, 2024

Conversation

SPPearce
Copy link
Contributor

Swapped the NGSCheckMate bed file for GRCh37.GATK to the one without "chr" prefix.

@SPPearce SPPearce changed the base branch from master to dev January 24, 2024 18:00
@nf-core nf-core deleted a comment from github-actions bot Jan 24, 2024
FriederikeHanssen
FriederikeHanssen approved these changes Jan 24, 2024
View reviewed changes
Copy link
Contributor

@FriederikeHanssen FriederikeHanssen left a comment

Choose a reason for hiding this comment

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

any upload to igenomes needed?

@github-actions GitHub Actions
Copy link

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

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 42d3fd0

+| ✅ 147 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • 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
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-24 18:02:02

@SPPearce
Copy link
Contributor Author

any upload to igenomes needed?

No, the file is already there and being used in Ensembl.GRCh37

@github-actions GitHub Actions
Copy link

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @SPPearce,

It looks like this pull-request is has been made against the nf-core/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@maxulysse maxulysse merged commit 0b5afa8 into dev Jan 25, 2024
60 of 80 checks passed
@maxulysse maxulysse deleted the ngscheckmate_fix branch February 15, 2024 17:27
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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

Successfully merging this pull request may close these issues.
3 participants
@SPPearce @FriederikeHanssen @maxulysse