AnVILWorkflow

AnVILWorkflow enables remote execution of bioinformatics workflows hosted on the Terra/AnVIL cloud platform directly from an R environment, facilitating access to large-scale genomics data and scalable computing resources through conventional R functions.

Key Features:

• Workflow Browsing: Users can browse available data and workflows hosted on AnVIL/Terra.
• R and Non-R Tool Integration: Enables seamless integration of R and non-R tools within a reproducible analysis pipeline.
• Scalable Computing Access: Provides accessibility to scalable computing resources without direct management overhead.
• Environment Setup: Simplifies the setup of the cloud computing environment for workflow execution.
• Input Data Formatting: Handles formatting of input data for workflow submission.
• Workflow Submission and Results Retrieval: Manages workflow submission and retrieval of results through R functions.

Scientific Applications:

• Bulk RNA-seq Analysis: Demonstrated for bulk RNA-seq analysis with Salmon.
• Metagenomics Analysis: Demonstrated for metagenomics analysis with bioBakery.
• Digital Pathology Image Processing: Demonstrated for digital pathology image processing with PathML.
• Exploratory Analyses: Supports exploratory analyses using established workflows.
• Bulk Processing: Supports bulk processing with established workflows.

Methodology:

AnVILWorkflow connects to Terra/AnVIL through R functions to execute cloud-implemented bioinformatics analysis pipelines.