Skip to content

Module/oncokb maf annotation - #189

Merged
johnoooh merged 18 commits into
developfrom
module/oncokb
Oct 29, 2025
Merged

Module/oncokb maf annotation#189
johnoooh merged 18 commits into
developfrom
module/oncokb

Conversation

@johnoooh

@johnoooh johnoooh commented Mar 4, 2025

Copy link
Copy Markdown
Collaborator

Adding a oncokb maf annotation module. I created the oncokb folder so we can add other oncokb scripts to it in the future, such as annotate CNV, among others. You need to add a oncokb token for this to work. I tested it locally with mine. Also, the container PR is here mskcc-omics-workflows/containers#27 but the module doesn't currently use this container, it uses a placeholder on my own dockerhub.

  • This comment contains a description of changes (with reason).
  • Check to see if a nf-core module, or subworkflow is available and usable for your pipeline.
  • Feature branch is named feature/<module_name> for modules, or feature/<subworkflow_name> for subworkflows. For modules, if there is a subcommand use: feature/<module_name>/<module_subcommand>.
  • 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.
  • Use nf-core data if possible for nf-tests. If not, use or add test data to mskcc-omics-workflows/test-datasets, following the repository guidelines, for nf-tests. Finally, if neither option is feasible, only add a stub nf-test.
  • 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 Jfrog if possible to fulfill software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile docker
      • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile singularity
      • nf-core modules --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <module_branch> test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows --git-remote https://github.com/mskcc-omics-workflows/modules.git -b <subworkflow_branch> test <SUBWORKFLOW> --profile conda

@johnoooh
johnoooh requested a review from a team as a code owner March 4, 2025 20:23
@johnoooh
johnoooh merged commit 89a7643 into develop Oct 29, 2025
20 checks passed
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.

3 participants