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

Implement Neo subworkflow #8

Merged
merged 23 commits into from
May 30, 2024
Merged

Implement Neo subworkflow #8

merged 23 commits into from
May 30, 2024

Commits on May 29, 2024

  1. Frame out Neo subworkflow

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    9898841 View commit details
    Browse the repository at this point in the history

  2. First cut of Neoepitope subworkflow

    @charlesshale @scwatts
    charlesshale authored and scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    70ccdad View commit details
    Browse the repository at this point in the history

  3. Get stub runs working

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    e9a04b3 View commit details
    Browse the repository at this point in the history

  4. Clean up

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    98ffac0 View commit details
    Browse the repository at this point in the history

  5. Get local run working on sample data

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    8b6df01 View commit details
    Browse the repository at this point in the history

  6. Set Neo to run only when specified

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    45226f3 View commit details
    Browse the repository at this point in the history

  7. Fix Neo stubs

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    37d18d5 View commit details
    Browse the repository at this point in the history

  8. Provide Neo cancer type from samplesheet

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    ea1fc26 View commit details
    Browse the repository at this point in the history

  9. Fix Neo scorer RNA sample ID and VCF input

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    cb94b8b View commit details
    Browse the repository at this point in the history

  10. Minor fixes

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    0f4cdda View commit details
    Browse the repository at this point in the history

  11. Update to latest Neo 1.2_beta build artefact

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    480dffb View commit details
    Browse the repository at this point in the history

  12. Update Neo reference data paths

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    efa42fb View commit details
    Browse the repository at this point in the history

  13. Move neo_prediction.nf subworkflow for consistency

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    ff6330b View commit details
    Browse the repository at this point in the history

  14. Adjust Neo to fit with alignment subworkflow 

    * add source selection for RNA BAM (samplesheet, alignment subworkflow)
* use appropriate function call to determine present of RNA
* relocate isofox_read_length assignment (wgts and targeted workflows)
    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    2b01ded View commit details
    Browse the repository at this point in the history

  15. Adjust indenting

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    92d95ad View commit details
    Browse the repository at this point in the history

  16. Indent Neo subworkflow to match nf-core style

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    c861d50 View commit details
    Browse the repository at this point in the history

  17. Use Bioconda for Neo annotate fusion process

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    0fde563 View commit details
    Browse the repository at this point in the history

  18. Add environment file for annotate fusion process

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    c367898 View commit details
    Browse the repository at this point in the history

  19. Rename some Neo subworkflow variables for clarity

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    f3be064 View commit details
    Browse the repository at this point in the history

  20. Add meta.yml for annotate fusion process

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    d997b37 View commit details
    Browse the repository at this point in the history

  21. Add meta.yml for Neo finder process

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    f46eacf View commit details
    Browse the repository at this point in the history

  22. Add meta.yml for Neo scorer process

    @scwatts
    scwatts committed May 29, 2024
    Configuration menu
    Copy the full SHA
    3cd29a9 View commit details
    Browse the repository at this point in the history

Commits on May 30, 2024

  1. Apply linting

    @scwatts
    scwatts committed May 30, 2024
    Configuration menu
    Copy the full SHA
    f1a365f View commit details
    Browse the repository at this point in the history