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 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.
• Python 3.8+: Install from Python's official website.
• 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

curl -s https://get.nextflow.io | bash

2. Install Python Dependencies

pip install -r requirements.txt

3. Configure Synapse (Optional)

# 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
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:

   nextflow secrets set SYNAPSE_AUTH_TOKEN your_personal_access_token

Usage

Input Format

The workflow accepts input in two formats:

1. Single Repository URL

nextflow run main.nf --repo_url https://github.com/example/repo.git

2. Sample Sheet (CSV)

Example input.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

nextflow run main.nf --repo_url https://github.com/example/repo.git

With AI Analysis

nextflow run main.nf \
    --repo_url https://github.com/example/repo.git \
    --synapse_agent_id LOWYSX3QSQ

With Sample Sheet

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:

• <repo_name>_ai_analysis.json: AI-powered qualitative summary and recommendations (final report)
• almanack_results.json: Detailed metrics from Almanack analysis
• joss_report_<repo_name>.json: JOSS criteria evaluation metrics
• test_results_<repo_name>.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	Python Optimal Transport Library	All checks pass
RabadanLab/TARGet	TARGet Analysis Tool	Fails dependency and test checks
arjunrajlaboratory/memSeqASEanalysis	memSeq ASE Analysis	Fails dependency and test checks

Configuration

Synapse Configuration

Authentication Token

• Set as Nextflow secret:

nextflow secrets set SYNAPSE_AUTH_TOKEN your_personal_access_token

Contributing

Note

We welcome contributions! Please see our Contributing Guidelines for details.

License

This project is licensed under the MIT License - see the LICENSE file for details.