PyPI 官网下载 | cidc_ngs_pipeline_api-0.1.10.tar.gz

# 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 │ ├── 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_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 ```