AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines

TL;DR

AnVILWorkflow is an R package that simplifies running bioinformatics workflows on the AnVIL cloud platform, making it easier for researchers to analyze large-scale genomic data.

Contribution

The package introduces a user-friendly interface for executing AnVIL workflows from R, enabling seamless integration of R and non-R tools in cloud-based analyses.

Findings

AnVILWorkflow supports bulk RNA-seq, metagenomics, and digital pathology use cases with established tools.

The package reduces the complexity of cloud computing setup and data formatting for non-expert users.

It enables reproducible and scalable analysis pipelines without requiring direct cloud infrastructure management.

Abstract

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. Here we present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflowsimplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflowfor three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. While some limitations exist around workflow customization, AnVILWorkflowlowers the barrier to taking advantage of AnVIL’s resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project (https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub (https://github.com/shbrief/AnVILWorkflow).

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