CIDC NGS Pipeline API

Overview

This repository serves as an interface between the CIDC and Bioinformatics teams to determine specifications and documentation related to NGS pipelines.

Repository structure:

.
├── README.md
├── cidc_ngs_pipeline_api
│   ├── output_API.schema.json
│   ├── rna
│   │   ├── rna.md
│   │   ├── rna_config.schema.json
│   │   ├── rna_output_API.json
│   │   └── imgs
│   |       └── RIMA.png
│   ├── atacseq
│   │   ├── atacseq.md
│   │   ├── atacseq_output_API.json
│   │   └── imgs
│   |       └── atacseq.png
│   ├── tcr
│   │   ├── tcr.md
│   │   └── imgs
│   |       └── TCRseq.png
│   └── wes
│       ├── wes.md
│       ├── wes_config.schema.json
│       ├── wes_output_API.json
│       ├── wes_tumor_only_output_API.json
│       ├── wes_output_API.py
│       └── imgs
│          └── wes.png
├── tests
│   └── test_apis.py
├── requirements.dev.txt
├── requirements.txt
├── MANIFEST.in
├── CHANGELOG.md
├── setup.py
└── .github
    └── workflows
       └── ci.yml
    

cidc_ngs_pipeline_api module

• The output_API.schema.json file defines the schema structure:

  • filter_group: Filter under which the file would appear during faceted search. It is the GCS-URI top-level hierarchy
  • file_path_template: Local file path used for CLI upload
  • short_description: Description to appear on hovering over file name in file browser
  • long_description: Longer description to appear on file documentation page
  • file_purpose: Assigns a tag to show up in a particular file-browser view configuration. Permissible values: Source view, Analysis view, Clinical view, Miscellaneous

• Within the directory for each assay:

  • The defined schema is used to structure information about pipeline-related files in the respective < assay >_output_API.json.

  • Information related to YAML configurations (which are generated by the CIDC and configured with CIMAC IDs to run the pipelines), are described in the respective < assay > config.schema.json.

  • Documentation related to each pipeline is in the respective < assay > .md.

Developer Setup

Install necessary dependencies.

pip install -r requirements.dev.txt

Install and configure pre-commit hooks.

pre-commit install