# CIDC NGS Pipeline API
 [](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
│ ├── 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.
```bash
pip install -r requirements.dev.txt
```
Install and configure pre-commit hooks.
```bash
pre-commit install
```
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"description": "# CIDC NGS Pipeline API\n\n [](https://opensource.org/licenses/MIT) \n\n### Overview\nThis repository serves as an interface between the CIDC and Bioinformatics teams to determine specifications and documentation related to NGS pipelines.\n\nRepository structure:\n```\n.\n\u251c\u2500\u2500 README.md\n\u251c\u2500\u2500 cidc_ngs_pipeline_api\n\u2502 \u251c\u2500\u2500 output_API.schema.json\n\u2502 \u251c\u2500\u2500 rna\n\u2502 \u2502\u00a0\u00a0 \u251c\u2500\u2500 rna.md\n\u2502 \u2502\u00a0\u00a0 \u251c\u2500\u2500 rna_config.schema.json\n\u2502 \u2502\u00a0\u00a0 \u251c\u2500\u2500 rna_output_API.json\n\u2502 \u2502\u00a0\u00a0 \u2514\u2500\u2500 imgs\n\u2502 | \u2514\u2500\u2500 RIMA.png\n\u2502 \u251c\u2500\u2500 atacseq\n\u2502 \u2502\u00a0\u00a0 \u251c\u2500\u2500 atacseq.md\n\u2502 \u2502\u00a0\u00a0 \u251c\u2500\u2500 atacseq_output_API.json\n\u2502 \u2502\u00a0\u00a0 \u2514\u2500\u2500 imgs\n\u2502 | \u2514\u2500\u2500 atacseq.png\n\u2502 \u251c\u2500\u2500 tcr\n\u2502 \u2502\u00a0\u00a0 \u251c\u2500\u2500 tcr.md\n\u2502 \u2502\u00a0\u00a0 \u2514\u2500\u2500 imgs\n\u2502 | \u2514\u2500\u2500 TCRseq.png\n\u2502 \u2514\u2500\u2500 wes\n\u2502 \u251c\u2500\u2500 wes.md\n\u2502 \u251c\u2500\u2500 wes_config.schema.json\n\u2502 \u251c\u2500\u2500 wes_output_API.json\n\u2502 \u251c\u2500\u2500 wes_tumor_only_output_API.json\n\u2502 \u251c\u2500\u2500 wes_output_API.py\n\u2502 \u00a0 \u2514\u2500\u2500 imgs\n\u2502 \u2514\u2500\u2500 wes.png\n\u251c\u2500\u2500 tests\n\u2502 \u2514\u2500\u2500 test_apis.py\n\u251c\u2500\u2500 requirements.dev.txt\n\u251c\u2500\u2500 requirements.txt\n\u251c\u2500\u2500 MANIFEST.in\n\u251c\u2500\u2500 CHANGELOG.md\n\u251c\u2500\u2500 setup.py\n\u2514\u2500\u2500 .github\n \u2514\u2500\u2500 workflows\n \u2514\u2500\u2500 ci.yml\n \n```\n\n## cidc_ngs_pipeline_api module\n\n* The `output_API.schema.json` file defines the schema structure:\n - `filter_group`: Filter under which the file would appear during faceted search. It is the GCS-URI top-level hierarchy\n - `file_path_template`: Local file path used for CLI upload\n - `short_description`: Description to appear on hovering over file name in file browser\n - `long_description`: Longer description to appear on file documentation page\n - `file_purpose`: Assigns a tag to show up in a particular file-browser view configuration. Permissible values: `Source view`, `Analysis view`, `Clinical view`, `Miscellaneous`\n \n* Within the directory for each assay:\n \n * The defined schema is used to structure information about pipeline-related files in the respective `< assay >_output_API.json`.\n\n * 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`.\n\n * Documentation related to each pipeline is in the respective `< assay > .md`.\n\n### Developer Setup\n\nInstall necessary dependencies.\n\n```bash\npip install -r requirements.dev.txt\n```\n\nInstall and configure pre-commit hooks.\n\n```bash\npre-commit install\n```\n",
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