Skip to content

oncocnv tentative switch to nf-test #8526

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.

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

Open
wants to merge 14 commits into
base: master
Choose a base branch
from
Open

oncocnv tentative switch to nf-test #8526

wants to merge 14 commits into from

Conversation

famosab
Copy link
Contributor

@famosab famosab commented May 21, 2025

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@famosab famosab linked an issue May 21, 2025 that may be closed by this pull request
@famosab famosab changed the title tentative switch to nf-test oncocnv tentative switch to nf-test May 21, 2025
Copy link
Contributor Author

@famosab famosab left a comment

Choose a reason for hiding this comment

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

I'll run nf-test

@famosab

This comment was marked as resolved.

@famosab
Copy link
Contributor Author

famosab commented May 22, 2025

│     Package 'mclust' version 6.1.1                                                                                                                                                                                                            │
│     Type 'citation("mclust")' for citing this R package in publications.                                                                                                                                                                      │
│     Package 'mclust' version 6.1.1                                                                                                                                                                                                            │
│     Type 'citation("mclust")' for citing this R package in publications.                                                                                                                                                                      │
│     Error: package or namespace load failed for ‘PSCBS’:                                                                                                                                                                                      │
│      .onLoad failed in loadNamespace() for 'R.cache', details:                                                                                                                                                                                │
│       call: mkdirs.default(parent, mustWork = mustWork, maxTries = maxTries,                                                                                                                                                                  │
│       error: Failed to create directory (tried 5 times), most likely because of lack of file permissions (directory '' exists but nothing beyond): /home-link                                                                                 │
│     In addition: Warning message:                                                                                                                                                                                                             │
│     In normalizePath("~") :                                                                                                                                                                                                                   │
│       path[1]="/home-link/paifb01": No such file or directory                                                                                                                                                                                 │
│     Execution halted  

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.

nf-test migration: oncocnv
2 participants