DITTO Clean Up and Local Prediction instructions by JmScherer · Pull Request #22 · uab-cgds-worthey/DITTO

Commits on Dec 12, 2025

Initial cleaning up the configs folder, organizing by service, and updating documentation to reflect new path
JmScherer
committed
Updating the configs folder for the nextflow configurations
JmScherer
committed
moved shap_plots to docs and removed hardcoded path from ./.test_data/file_list.txt
JmScherer
committed
Update the model.job with some changes and the pipeline.nf
JmScherer
committed
Moved oc ditto package into config/opencravat
JmScherer
committed
Updated readme
JmScherer
committed

Commits on Dec 15, 2025

Commits on Dec 16, 2025

Commits on Dec 18, 2025

Commits on Jan 6, 2026

Markdown linting for README
JmScherer
committed

Commits on Jan 7, 2026

Added ditto-env.yaml to conda envs, updated README to reflect, and added names to other environments
JmScherer
committed

Commits on Jan 8, 2026

Commits on Jan 15, 2026

Updated the ditto-nf.yaml conda env to include h5py binary as it was throwing errors. We suspect the version it pulled automatically was too new for the pipeline
JmScherer
committed

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DITTO Clean Up and Local Prediction instructions#22

DITTO Clean Up and Local Prediction instructions#22
JmScherer wants to merge 24 commits intomainfrom
local-prediction

Commits on Dec 12, 2025

Initial cleaning up the configs folder, organizing by service, and updating documentation to reflect new path

Updating the configs folder for the nextflow configurations

moved shap_plots to docs and removed hardcoded path from ./.test_data/file_list.txt

Update the model.job with some changes and the pipeline.nf

Moved oc ditto package into config/opencravat

Updated readme

Commits on Dec 15, 2025

Updating the README.md

More README.md updates

Markdown linting on README.md

Hopefully finished README markdown linting

Updated README.md to include local.config for local prediction instructions and updated the .gitignore to ignore the work_dir for temporary nextflow runs

Commits on Dec 16, 2025

Worked out an output directory path and updated the documentation

fixing ./text_data/file_list.txt

Updating model.job output folder

updating the folder for output on nextflow command

Commits on Dec 18, 2025

Update pipeline.nf

Update README.md

Update README.md

Update README.md

Commits on Jan 6, 2026

Markdown linting for README

Commits on Jan 7, 2026

Added ditto-env.yaml to conda envs, updated README to reflect, and added names to other environments

Commits on Jan 8, 2026

Updated the README to discuss relative and absolute pathing for the file_list.txt for pathing on vcfs for DITTO; Updated README to discuss the use of Mamba for NextFlow

markdown linting

Commits on Jan 15, 2026

Updated the ditto-nf.yaml conda env to include h5py binary as it was throwing errors. We suspect the version it pulled automatically was too new for the pipeline