3 posts tagged with "ci-cd"

Building reproducible bioinformatics pipelines is hard. Every project starts from scratch with its own testing, CI/CD, and deployment strategy. What if you could clone a template, add your analysis tools, and be ready to go?

This post introduces a standardized bioinformatics workflow template featuring consistent testing, CI/CD, and project structure. Developed from real production experience with bioinfor-wf-template, this template reduces setup time from days to minutes, ensures research reproducibility, and promotes modular, reusable code. It is Python-based and ideal for proof-of-concept projects. Support for more advanced and widely adopted bioinformatics frameworks (such as Snakemake and Nextflow) is planned, applying the same core principles while leveraging their native testing systems.

GitHub Actions are powerful for automating bioinformatics pipelines, but waiting 5-10 minutes for each cloud run is painful during development. act lets you run GitHub Actions workflows locally on your machine in seconds, slashing feedback time by 5x.

In this post, we'll explore act, a command-line tool that runs GitHub Actions locally using Docker. Perfect for testing ML pipelines, gene expression analysis, and CI/CD workflows before pushing to GitHub.

Welcome to Part 2 of our series on version control in bioinformatics. In Part 1, we introduced Git fundamentals, branching strategies, and collaborative workflows. In this post, we'll dive into how Continuous Integration and Continuous Deployment (CI/CD) can transform your bioinformatics projects. If these concepts are new to you, don't worry—this guide will walk you through managing your bioinformatics repository to ensure your work is easily reproducible on any machine. Whether your server is wiped or you need to spin up a new virtual machine, you'll be able to quickly rerun your pipeline. With CI/CD, every code update can automatically trigger tests on a small dataset to verify everything works before scaling up, ensuring that new changes don't break your results or workflows.