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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
Containers
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
A Toy Example
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
What We Have
Extend to CUTADAPT → BWA_ALIGN → FREEBAYES
Workflow for CUTADAPT → BWA_ALIGN → FREEBAYES
Additional Links
Saving Document Versions
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