Week 6: Pipelines


2 Content overview

In this final week with new content, you will be learning about informal and formal (bioinformatics analysis) pipelines, and using a best-practice pipeline written with the Nextflow workflow management system by the nf-core initiative.

Some of the things you will learn this week

  • Get a better understanding of the purpose and mechanics of “runner scripts”.
  • What challenges you can run into when creating analysis pipelines with regular Bash scripts, including runner scripts.
  • What “workflow management systems” like Snakemake and Nextflow are, and what the advantages of formal pipelines written with these are.
  • What the nf-core initiative is, and how you can run one of their pipelines at OSC.

Required readings

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