CCKP Toolkit Workflow

Description

This Nextflow workflow (main.nf) performs quality and metadata checks on software tools by running a series of checks:

• CloneRepository: Clones the repository.
• CheckReadme: Verifies the existence of a README file.
• CheckDependencies: Looks for dependency files (e.g., requirements.txt, Pipfile, setup.py, etc.).
• CheckTests: Checks for the presence of test directories or test files.
• CheckAlmanack: Runs the Software Gardening Almanack analysis.

The final output is a consolidated CSV report where each row represents a tool (i.e., a repository) with the following columns:

Tool, CloneRepository, CheckReadme, CheckDependencies, CheckTests, Almanack

Each column shows the status (PASS/FAIL) for the respective check.

Running the Workflow

You can execute the workflow in one of two ways:

• Analyze a single tool by specifying its repository URL.
• Analyze multiple tools using a sample sheet (CSV file) that includes a repo_url header.

Install Nextflow

Follow the official installation guide here or use the command below:

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

Run with a Single Repository URL

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

Run with a Sample Sheet

Prepare a CSV file (e.g., example-input.csv) with a header repo_url and one URL per row, then run:

nextflow run main.nf --sample_sheet <samplesheet>

Output

After the workflow completes, you'll find a consolidated CSV report (consolidated_report.csv) in your output directory (by default, under the results folder). Each row in this report represents a tool and its corresponding check statuses.

Optional: Uploading Results to Synapse

To upload results to Synapse, run the workflow with the following parameters:

nextflow run main.nf \
    --repo_url https://github.com/example/repo.git \
    --upload_to_synapse true\
    --synapse_folder_id syn64626421

Ensure your Synapse credentials are properly set up (e.g., by mounting your .synapseConfig file).

Tools You Can Test With

1. Python Optimal Transport Library

   • Synapse: POT
   • GitHub: PythonOT/POT
   • Note: Should pass all tests

2. TARGet

   • Synapse: TARGet
   • GitHub: RabadanLab/TARGet
   • Note: Fails CheckDependencies, CheckTests

3. memSeqASEanalysis

   • Synapse: memSeqASEanalysis
   • GitHub: arjunrajlaboratory/memSeqASEanalysis
   • Note: Fails CheckDependencies, CheckTests

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

Notes

• Ensure Nextflow and Docker are installed