Skip to content

Fix CI: Remove oncokb_genes file dependency and use process substitution - #1052

Merged
gongyixiao merged 3 commits into
developfrom
bugfix/ci-test
Feb 6, 2026
Merged

Fix CI: Remove oncokb_genes file dependency and use process substitution#1052
gongyixiao merged 3 commits into
developfrom
bugfix/ci-test

Conversation

@gongyixiao

@gongyixiao gongyixiao commented Feb 5, 2026

Copy link
Copy Markdown
Collaborator

CI Fixes

Cleanup work for #1042 and #1043

  • Remove oncokb_genes file dependency by using empty files
  • Resolved the 'Process Substitution' error in `SomaticAnnotateMaf.nf` by ensuring POSIX compliance (using empty files instead of `<(echo ...)`).
  • Update CI workflow to use Ubuntu 24.04 to avoid no space left on device issue

@netlify

netlify Bot commented Feb 5, 2026

Copy link
Copy Markdown

Deploy Preview for cmotempo failed. Why did it fail? →

⚠️ Continuous deployment needs attention — organization-owned private repository detected.
Upgrade to Pro or change repository settings in order to continue deploying from this repository.
For more information, visit the deploy log and FAQ page.

Name Link
🔨 Latest commit ebebcfa
🔍 Latest deploy log https://app.netlify.com/projects/cmotempo/deploys/69850d067b2d0d00083657cd

@gongyixiao
gongyixiao marked this pull request as ready for review February 5, 2026 18:58
@gongyixiao
gongyixiao merged commit ef39363 into develop Feb 6, 2026
1 of 5 checks passed
@gongyixiao
gongyixiao deleted the bugfix/ci-test branch February 6, 2026 04:08
@gongyixiao gongyixiao mentioned this pull request Feb 6, 2026
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant