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Nextflow run for Imaging

This training course is intended for researchers in imaging and spatial biology who are interested in running and customizing data analysis pipelines. It teaches foundational Nextflow concepts related to running, organizing and configuring workflows using nf-core/molkart, a pipeline for processing Molecular Cartography spatial transcriptomics data. The skills you learn here are transferable to any Nextflow or nf-core pipeline.

Let's get started! Click on the "Open in GitHub Codespaces" button below to launch the training environment (preferably in a separate tab), then read on while it loads.

Open in GitHub Codespaces

Learning objectives

By working through this course, you will learn how to apply foundational Nextflow concepts and tooling to running imaging analysis pipelines.

By the end of this workshop you will be able to:

  • Launch a Nextflow workflow locally and monitor execution
  • Find and interpret outputs (results) and log files generated by Nextflow
  • Run an nf-core pipeline with test data and custom inputs
  • Configure pipeline execution using profiles and parameter files
  • Manage inputs using samplesheets and command-line parameters

Audience & prerequisites

This course assumes some minimal familiarity with the following:

  • Experience with the command line
  • Basic familiarity with imaging file formats (TIFF images, tabular data)

For technical requirements and environment setup, see the Environment Setup mini-course.