Prerequisites

Get Started Quickly:

This document outlines the various methods to import your Nextflow pipeline on Basepair platform for efficient and streamlined analysis.

1. Package Your Pipeline

        a. Public GitHub Repository:

• If your pipeline is publicly available on GitHub, Basepair can directly access and utilize it at the Module YAML level. This is the most straightforward approach for public pipelines.
  

        b. Private GitHub Integration :

• Basepair has developed a feature that allows for direct integration with private GitHub repositories using a GitHub access token. This enables users to easily install the Basepair GitHub app through the "Integrations" tab within the "Organization Settings" section of their user profile on the Basepair platform

2. Database & Reference Files (Optional)

• This section pertains to specific scenarios where your pipeline relies on:

- Proprietary databases

- Reference genome files

• If your pipeline necessitates these resources, you can upload them to the same S3 bucket you used for your pipeline archive. This ensures Basepair has all necessary components for successful analysis.

Alternatively, you can leverage Basepair's pre-uploaded genome files. These files will be attached as metadata to each sample object, simplifying the process.

3. Docker Image Access

• Currently, Basepair requires access to your private Dockerfile stored in a secure location like Amazon ECR (Elastic Container Registry). This Dockerfile provides instructions for building the containerized environment necessary for your pipeline's execution.

Basepair puts user-friendliness first, even for secure private images. New feature coming for streamlined, secure pulling docker images. 

4.  Basepair API Setup:

• Refer to Basepair's documentation for comprehensive instructions on setting up API to interact with the platform
  SETUP