cidc-ngs-pipeline-api 0.1.21

The CIDC NGS Pipeline output APIs

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
│   ├── chips
│   │   ├── chips.md
│   │   ├── chips_output_API.json
│   │   └── imgs
│   |       └── chips.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
├── setup.cfg
├── 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