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.

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

Update genomescope2 module and add nf-tests #5399

Merged
merged 10 commits into from
Mar 26, 2024
Merged

Conversation

mahesh-panchal
Copy link
Member

PR checklist

  • Updates module container builds
  • Adds output for --fitted_hist
  • Migrates pytest to nf-test.

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

@mahesh-panchal mahesh-panchal requested a review from a team as a code owner March 26, 2024 16:55
@mahesh-panchal mahesh-panchal requested review from LeuThrAsp and rodtheo and removed request for a team March 26, 2024 16:55
@mahesh-panchal mahesh-panchal added this pull request to the merge queue Mar 26, 2024
Merged via the queue into master with commit 9bc4822 Mar 26, 2024
11 checks passed
@mahesh-panchal mahesh-panchal deleted the nftest_genomescope2 branch March 26, 2024 19:14
jvfe added a commit that referenced this pull request Mar 26, 2024
* master: (47 commits)
  Update genomescope2 module and add nf-tests (#5399)
  PLINK/GWAS additional output (#5387)
  Plink linkage disequilibrium additional output (#5388)
  new module: Plink epistasis analysis  (#5386)
  Add module for TaxonKit name2taxid (#4778)
  Update-cellranger-modules (#5016)
  Update: GTDBTK/CLASSIFYWF (migrate to nf-test and only execute mv when dirs actually present) (#5390)
  Added MetaPlAn subworkflow (#5356)
  port `vcftools` to nf-test (#5375)
  Update modules: rgi (#5383)
  Update condaforge/mambaforge Docker tag to v24 (#5381)
  Update gecco + migrate to nf-test (#5372)
  Update learnmsa module to work with compressed files. (#5276)
  New module: kraken2/build  (#5212)
  Update kalign module to work with compressed files. (#5277)
  port `ensemblvep/download` to nf-test (#5373)
  port `manta-germline` to nf-test (#5362)
  port `tiddit-sv` to nf-test and add `--threads` (#5371)
  Decoupler module (#5317)
  fix optional cram support in modules and migrate to nf-test (#5329)
  ...
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.

2 participants