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Computational Workflows

Coming soon — July 2026

This workshop is under development and will be available for the July 2026 workshop series. Check back closer to the session date for the full course page.

Bioinformatics analyses are rarely a single script — they are pipelines: sequences of tools that each transform data from one format to another, from raw sequencing reads all the way to count matrices or variant calls. Workflow management systems like Nextflow make these pipelines reproducible, portable, and scalable across laptops, HPC clusters, and cloud environments.

In this workshop you will learn the principles behind bioinformatics workflows, explore the nf-core collection of community-maintained pipelines, and run an end-to-end RNA-seq pipeline against real data on a cloud or HPC environment.

Topics Covered

  • What a bioinformatics pipeline is and why workflow managers matter
  • Core concepts in Nextflow: processes, channels, and executors
  • The nf-core ecosystem: curated, peer-reviewed pipelines
  • Running nf-core/rnaseq: inputs, configuration, and outputs
  • Understanding pipeline output: what each file is and where it goes
  • Scaling from local to cloud and HPC execution
  • Resuming and debugging failed runs

Prerequisites

  • Completion of the Introduction to Data Science series, or equivalent experience
  • Familiarity with the command line is helpful but not required

Questions? Contact the CGDS Core — CGDS@mdibl.org