Metadata-Version: 2.1
Name: cidc_ngs_pipeline_api
Version: 0.1.11
Summary: The CIDC NGS Pipeline output APIs
Home-page: https://github.com/CIMAC-CIDC/cidc-ngs-pipeline-api
Author: Stephen C van Nostrand
Author-email: vannost@ds.dfci.harvard.edu
License: MIT license
Description: # CIDC NGS Pipeline API
        
        ![Continuous Integration](https://github.com/CIMAC-CIDC/cidc-ngs-pipeline-api/workflows/Continuous%20Integration/badge.svg?branch=master)  [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) 
        
        ### 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
        │   ├── 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.
        
        ```bash
        pip install -r requirements.dev.txt
        ```
        
        Install and configure pre-commit hooks.
        
        ```bash
        pre-commit install
        ```
        
Keywords: cidc_ngs_pipeline_api
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.6
Description-Content-Type: text/markdown
