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Reproducibility in Bioinformatics

Reproducibility in Science

The Reproducibility Problem

Studies in Reproducibility

Challenges of Bioinformatics

Aspects of Reproducibility

Saving Document Versions

Version Control

Environment Management

Storing Results

Bioinformatic Pipelines

Bioinformatic Pipeline Challenges

Bioinformatic Pipelines on HPC

Snakemake

Snakemake Format

Snakemake Core Idea

Recommended Pipeline Directory Structure

Snakefile Breakdown

Example Snakefile

Snakemake Exercises on HPC

Running jobs on interactive node

Modules

Other Modules Needed

Running snakemake - genome alignment

Running Snakemake - Variant Detection

Snakemake Examples on HPC

Running Snakemake with Config File

Reproducible Environments

Using Environments

Snakemake with Conda Environment

Smakemake and containers

Best Practices for HPC

Common HPC Pitfalls with Workflow Managers

Key Takeaways with Workflow Managers

Nextflow

What is Nextflow?

Nextflow Pipelines

Create a New File called main.nf

Make Some Changes

Add a publishDir

Look at a Trim Rule

What to Update in Nextflow?

Update for Running Cutadapt

A More Common Approach

Dynamically Scaling to Many Samples

Parameter Options for Input Files

Less Hard-coding = More Reproducibility

Loading Software

Loading Software – nextflow.config

Adding SLURM Options

Extend to CUTADAPT → BWA_ALIGN → FREEBAYES

Workflow for CUTADAPT → BWA_ALIGN → FREEBAYES

Additional Links

Nextflow

Snakemake & Nextflow provide:

reproducible pipelines
automatic dependency tracking
scalable HPC execution
environment management
workflow portability

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Key Takeaways with Workflow Managers

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What is Nextflow?

Last updated on Mar 25, 2026

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