├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── config.yml │ ├── feature_request.md │ └── new_task.yml ├── PULL_REQUEST_TEMPLATE.md ├── dependabot.yml └── workflows │ ├── build.yml │ └── test.yml ├── .gitignore ├── .gitmodules ├── .vscode └── settings.json ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── _viash.yaml ├── main.nf ├── nextflow.config ├── scripts ├── create_resources │ ├── reprocess_task_results_v4.sh │ ├── task_results_v1.sh │ ├── task_results_v2.sh │ ├── task_results_v3.sh │ └── task_results_v4.sh └── sync_resources.sh └── src ├── datasets └── README.md ├── project ├── create_component │ ├── config.vsh.yaml │ ├── script.py │ └── test.py ├── fetch_run_work_dir │ ├── config.vsh.yaml │ └── script.sh ├── render_readme │ ├── config.vsh.yaml │ ├── script.R │ └── test.R ├── sync_resources │ ├── config.vsh.yaml │ ├── script.sh │ └── test.sh └── upgrade_config │ ├── config.vsh.yaml │ ├── script.py │ └── test.py ├── reporting ├── combine_output │ ├── config.vsh.yaml │ └── script.R ├── filter_results │ ├── config.vsh.yaml │ └── script.py ├── generate_qc │ ├── config.vsh.yaml │ └── script.R ├── get_dataset_info │ ├── config.vsh.yaml │ └── script.R ├── get_method_info │ ├── config.vsh.yaml │ └── script.R ├── get_metric_info │ ├── config.vsh.yaml │ └── script.R ├── get_results │ ├── config.vsh.yaml │ └── script.R ├── get_task_info │ ├── config.vsh.yaml │ └── script.R ├── process_dataset_metadata │ ├── config.vsh.yaml │ ├── main.nf │ └── run.sh ├── process_task_results │ ├── config.vsh.yaml │ ├── main.nf │ ├── run_nf_tower_test.sh │ └── run_test.sh ├── render_report │ ├── config.vsh.yaml │ ├── logo.svg │ ├── report-functions.R │ ├── report-template.qmd │ └── script.R └── shared │ ├── bibliography.bib │ └── functions.R ├── tasks ├── batch_integration │ └── README.md ├── denoising │ └── README.md ├── dimensionality_reduction │ └── README.md ├── label_projection │ └── README.md ├── match_modalities │ └── README.md ├── 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