All courses Workflow Academy · Course 03 · Advanced

Developing pipelines on the platform: advanced

Take pipelines to production. Govern, scale and validate workflows for regulated R&D environments with full audit trails.

Course overview

What you will cover

Six modules over two sessions of four hours each, with hands-on labs throughout.

Module 01

Production-grade module design

Defensive defaults, typed schemas, fail-fast behaviour
Container image strategy and reproducibility
Module testing patterns and CI

Module 02

Scaling workflows on the platform

Compute targets at scale: HPC, Seqera, cloud burst
Resource configuration, retries and checkpointing
Profiling and cost-aware optimisation

Module 03

Governance and version control

Locking workflows for production
Release management, semantic versioning, deprecation
Sign-off and change control

Module 04

Audit trails and compliance

Audit-by-construction in Viash and Nextflow
GAMP 5, FDA 21 CFR Part 11 and ISO 13485 in practice
Evidence generation for submissions and audits

Module 05

Multi-team patterns

Shared catalogues and team workspaces
Access control, secrets and data sovereignty
Cross-team workflow reuse

Module 06

Integration and the AI surface

API access, webhooks and LIMS integration
Designing workflows that AI agents can use safely
Roadmap: governed AI authoring

Objectives

What you will achieve

Ship pipelines that meet regulated R&D requirements out of the box.
Govern workflows across teams with versioning, sign-off and audit trails.
Scale pipelines from a single sample to atlas-scale workloads.

Key take-aways

By the end of the course

You can take a pipeline from prototype to production on the platform. Audit-ready, governed across teams, scalable from a laptop to a cluster, ready for the AI surface that's coming.

Required skills

Before you start

Completed Course 02 or equivalent hands-on Viash and Nextflow experience. Familiar with version control (Git) and container tooling.

Trainers

Led by

Data Intuitive bioinformatics teamWorking bioinformatics engineers

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