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CCKP Toolkit Workflow README

Description

This Nextflow workflow main.nf performs a high-level quality check on tools. The workflow consists of the following processes:

  1. CloneRepository: Clones a Git repository from the provided URL into a temporary directory and copies the repository to a designated location.

  2. CheckReadme: Checks the cloned repository for the presence of a README file. It looks for various common README file names and reports whether one was found.

  3. CheckDependencies: Scans the repository for dependency files associated with different programming languages. It reports the presence of files for Python, JavaScript/Node.js, Java, and R.

  4. CheckTests: Looks for test directories or files within the repository.

  5. CheckAlmanack: Implements the Software Gardening Almanack to gather various metrics about the repository.

    • Note: The CheckAlmanack process now uses python3 to execute the Python command. If you encounter issues, ensure that Python 3 is installed and that python3 is in your system's PATH.

  6. SaveToSynapse (Optional): Uploads workflow results of the toolkit to a specified Synapse folder if the upload option is enabled.

Setup

Install Nextflow:

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

Install Almanack:

pip install almanack

Configuration

You can configure the workflow using nextflow.config. Set your working directory here.

Usage

To run the workflow, you need to provide the URL of the Git repository you want to analyze as a parameter. Here's how you can execute the workflow:

nextflow run main.nf --repo_url <repository-url>

Replace <repository-url> with the URL of the Git repository you wish to check.

Example

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

To upload results to Synapse

nextflow run main.nf \
    --repo_url https://github.com/PythonOT/POT.git \
    --upload_to_synapse true \
    --synapse_folder_id syn64626421 \
    -with-trace trace.txt

Docker Usage

You may also use Docker to run the CCKP Toolkit Workflow as an alternative to the above. First, install Docker on your system. Then, use the commands below as an example of how to run the workflow.

# Build an image for the CCKP Toolkit Workflow
docker build -t cckp-toolkit-workflow .

# Run the image for the CCKP Toolkit Workflow, passing in a Git repository URL
docker run cckp-toolkit-workflow https://github.com/mc2-center/cckp-toolkit-workflow

Tools You Can Test With

  1. Python Optimal Transport Library

  2. TARGet

  3. memSeqASEanalysis

Subset of tools to test: Any from this list with a GitHub repository.

Notes

Ensure Git is installed on your system as the workflow uses git clone to clone the repository. The workflow assumes the repository is public or accessible with the provided URL.