https://github.com/mc2-center/cckp-toolkit-workflow
This Nextflow workflow main.nf performs a high-level quality check on tools.
https://github.com/mc2-center/cckp-toolkit-workflow
computational-biology software
Last synced: 5 days ago
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This Nextflow workflow main.nf performs a high-level quality check on tools.
- Host: GitHub
- URL: https://github.com/mc2-center/cckp-toolkit-workflow
- Owner: mc2-center
- Created: 2024-06-18T17:34:31.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-12-03T18:49:25.000Z (about 2 months ago)
- Last Synced: 2025-12-06T19:09:06.686Z (about 2 months ago)
- Topics: computational-biology, software
- Language: Python
- Homepage:
- Size: 1.21 MB
- Stars: 2
- Watchers: 2
- Forks: 2
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
# Cancer Complexity Toolkit Workflow
## Description
The Cancer Complexity Toolkit Workflow is a scalable infrastructure framework to promote sustainable tool development. It performs multiple levels of analysis:
1. **Basic Repository Checks**
- Repository cloning and validation
- README file verification
- Dependency file detection
- Test suite presence
2. **Advanced Analysis**
- [Software Gardening Almanack](https://github.com/software-gardening/almanack) analysis
- JOSS (Journal of Open Source Software) criteria evaluation
- AI-powered repository analysis (optional, requires Synapse agent ID)
- Test execution and coverage
3. **Optional Synapse Integration**
- Results upload to Synapse platform
- Metadata management
## Requirements
### Core Dependencies
- **Nextflow** (version 24.04.3 or later): Install from [Nextflow's official website]. Install instructions below (https://www.nextflow.io/).
- **Docker** (required for containerized execution): Install from [Docker's official website](https://www.docker.com/get-started).
- **Python 3.8+**: Install from [Python's official website](https://www.python.org/downloads/).
- **Git**
> [!IMPORTANT]
> Docker is required to run this workflow. The toolkit uses containerized processes to ensure consistent execution environments across different systems.
### Optional Dependencies
For Synapse integration:
- Synapse Python client
- Synapse authentication token
- Synapse configuration file
## Installation
1. **Install Nextflow**
```bash
curl -s https://get.nextflow.io | bash
```
2. **Install Python Dependencies**
```bash
pip install -r requirements.txt
```
3. **Configure Synapse** (Optional)
```bash
# Create Synapse config file
mkdir -p ~/.synapse
touch ~/.synapseConfig
```
> [!NOTE]
> To use Synapse features, you'll need to:
> 1. Create a personal access token from your [Synapse Account Settings](https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens)
> 2. Add the token to your `~/.synapseConfig` file:
> ```
> [authentication]
> username = your_username
> apiKey = your_personal_access_token
> ```
> 3. Set the token as a Nextflow secret:
> ```bash
> nextflow secrets set SYNAPSE_AUTH_TOKEN your_personal_access_token
> ```
## Usage
### Input Format
The workflow accepts input in two formats:
1. **Single Repository URL**
```bash
nextflow run main.nf --repo_url https://github.com/example/repo.git
```
2. **Sample Sheet (CSV)**
Example `input.csv`:
```csv
repo_url,description
https://github.com/PythonOT/POT.git,Python Optimal Transport Library
https://github.com/RabadanLab/TARGet.git,TARGet Analysis Tool
```
### Running the Workflow
#### Basic Analysis
```bash
nextflow run main.nf --repo_url https://github.com/example/repo.git
```
#### With AI Analysis
```bash
nextflow run main.nf \
--repo_url https://github.com/example/repo.git \
--synapse_agent_id LOWYSX3QSQ
```
#### With Sample Sheet
```bash
nextflow run main.nf --sample_sheet input.csv
```
> [!NOTE]
> When using AI Analysis or Synapse integration, ensure you have:
> - Valid Synapse authentication token
> - Proper Synapse configuration
> - Synapse agent ID for AI analysis (e.g., LOWYSX3QSQ)
> - Correct folder ID with write permissions (for upload)
## Output
The workflow generates several output files in the `results` directory:
- `_ai_analysis.json`: AI-powered qualitative summary and recommendations (final report)
- `almanack_results.json`: Detailed metrics from Almanack analysis
- `joss_report_.json`: JOSS criteria evaluation metrics
- `test_results_.json`: Test execution results and coverage metrics
> [!NOTE]
> The AI analysis report provides a high-level qualitative summary and actionable recommendations. For detailed metrics and specific measurements, refer to the other output files.
## Development Status
> [!WARNING]
> The AI Analysis component is currently in beta. Results may vary and the interface is subject to change.
> [!IMPORTANT]
> Synapse integration requires proper authentication and permissions setup.
## Example Repositories
| Repository | Description | Expected Status |
|------------|-------------|----------------|
| [PythonOT/POT](https://github.com/PythonOT/POT) | Python Optimal Transport Library | All checks pass |
| [RabadanLab/TARGet](https://github.com/RabadanLab/TARGet) | TARGet Analysis Tool | Fails dependency and test checks |
| [arjunrajlaboratory/memSeqASEanalysis](https://github.com/arjunrajlaboratory/memSeqASEanalysis) | memSeq ASE Analysis | Fails dependency and test checks |
## Configuration
### Synapse Configuration
**Authentication Token**
- Set as Nextflow secret:
```bash
nextflow secrets set SYNAPSE_AUTH_TOKEN your_personal_access_token
```
## Contributing
> [!NOTE]
> We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
## License
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.