Nextflow is a powerful and flexible workflow management system that supports various types of pipelines.


This brief document outlines the requirements and considerations for integrating Nextflow pipeline with Basepair. The integration will allow users to run their Nextflow pipelines on the Basepair platform, leveraging the benefits of cloud-based computing infrastructure and enhanced data management capabilities. Maximize your workflow efficiency with Basepair's versioning , allowing you to effortlessly switch between pipeline versions.

1. Prerequisites

2. Pipeline & Module YAML Creation

Custom Nextflow pipeline integration on basepair is almost ready to go live!

  • Direct FASTQ Upload to BP!
    • Upload your raw FASTQ files directly to BP via GUI/CLI/Basespace.
    • No need to create a separate SampleSheet CSV file - we'll generate it automatically during analysis.
  • Ready to test? Login to BP platform and kick off some analysis to validate your integration

You'll be able to monitor the progress of your analysis and access the results when it's complete.