Pipelines

Many commonly used best-practices piplines are available for a variety of genomic assays including bulk and single-cell RNA-seq, WGS, WES/panel, ATAC-seq, CUT&RUN, CUT&TAG, ChIP-seq, metagenomics and more! Users may add their own custom pipelines as well.

📄️ Add docker pipeline

Creating a custom workflow on Basepair

📄️ Add nextflow pipeline

Nextflow Integration

📄️ Custom Pipeline

1. Introduction

📄️ Custom Modules

The Module feature allows users to create, manage, and reuse modules that can be integrated into pipelines. These modules define reusable commands, inputs, and outputs for various analysis tasks.

📄️ Pipeline YAML

You may configure the pipeline parameters in a YAML file.

📄️ Add docker pipeline

📄️ Add nextflow pipeline

📄️ Custom Pipeline

📄️ Custom Modules

📄️ Pipeline YAML

📄️ Module YAML