Pipeline Engine

bioAF includes a built-in pipeline execution engine that lets you run bioinformatics workflows without managing compute infrastructure.

Pipeline catalog

bioAF ships with pre-configured nf-core pipelines:

• nf-core/scrnaseq: Single-cell RNA-seq analysis
• nf-core/rnaseq: Bulk RNA-seq quantification
• nf-core/atacseq: ATAC-seq peak calling and analysis
• Custom pipelines can be added by providing a Git repository URL

i What is nf-core?

nf-core is a community effort to collect, curate, and maintain high-quality Nextflow pipelines for bioinformatics. These pipelines are peer-reviewed, well-tested, and follow best practices. bioAF makes them available with one-click launching.

Launching a run

Select a pipeline, choose your experiment and samples, configure any parameter overrides, and launch. bioAF handles:

• Scheduling compute resources
• Staging input data
• Executing the workflow
• Collecting outputs to the results bucket
• Notifying you when it’s done

Real-time monitoring

Every running pipeline shows:

• Stage-by-stage status: See which steps are complete, running, or queued
• DAG visualization: A visual graph of the workflow structure
• Resource usage: CPU, memory, and timing per stage
• Live logs: Stream logs from any running stage

Outputs and results

When a pipeline completes, outputs are automatically:

• Stored in the results bucket
• Linked to the originating experiment and samples
• Available for QC dashboards and visualization
• Recorded in the audit log with full parameter provenance