CI/CD in Bioinformatics Pipelines — Hands-on

Deliver bioinformatics workflows with software-engineering rigor. This module shows how to build continuous integration and delivery systems for Snakemake/Nextflow/Galaxy pipelines—automated testing with golden datasets, container builds and security scans, artifact/version management, policy gates, and push-button deployments across HPC and Cloud.

CI/CD in Bioinformatics Pipelines

Help Desk · WhatsApp

Session Index

Session 1 — Git, CI Basics & Testable Pipelines Session 2 — Containers, Artifacts & Security Scans Session 3 — Releases, Policies & Environments Session 4 — Mini Capstone: Prod-Ready CI/CD

Session 1

Fee: Rs 16,400

Git, CI Basics & Testable Pipelines

Git workflow & CI runners

GitHub Actions GitLab CI Jenkins

Make pipelines testable

golden datasets unit/integration tests smoke runs

Caching & speed-ups

conda/mamba locks artifact reuse matrix builds

Session 2

Fee: Rs 22,000

Containers, Artifacts & Security Scans

Build & publish images

Docker/Apptainer multi-arch buildx GHCR/ECR/GCR

Security & provenance

Trivy/Grype scans SBOM (CycloneDX/Syft) Cosign/SLSA attestations

Artifacts & reports

MultiQC PDFs result manifests dataset registries

Session 3

Fee: Rs 27,600

Releases, Policies & Environments

Versioning & changelogs

semver/tags release notes backports/LTS

Policy-as-code & quality gates

OPA/Conftest Great Expectations required checks

Environments & secrets

dev→staging→prod secrets managers RBAC/IAM

Session 4

Fee: Rs 34,200

Mini Capstone: Prod-Ready CI/CD

Implement CI/CD for a real pipeline (Snakemake/Nextflow)

Theory + Practical

Deploy to HPC/Cloud safely

blue-green/canary rollbacks observability

Deliverables: repo, CI/CD config & release assets

pipelines + tests container images PDF/HTML runbook

PDF

CI/CD in Bioinformatics Pipelines Training | Testing, Security, Releases & Deployments

CI/CD in Bioinformatics Pipelines — Hands-on