Modular, reproducible bioinformatics workflows with the {targets} R package

Modern bioinformatics pipelines can be incredibly complex, but all tend to follow a common pattern: they start with raw data, then pass the data through various programs until arriving at a final result. If this is done in an ad-hoc, unorganized fashion, the results may never be reproducible or even worse, unreliable and/or wrong. Pipeline management software is therefore essential to obtain results that are robust and reproducible. The targets R package is a recently developed workflow manager that comes with many excellent features for bioinformatics, including data caching, pipeline-level parallelization, and HPC support. In this hands-on workshop, I will demonstrate how targets can be used in concert with other tools like docker and conda to orchestrate modular, reproducible bioinformatics pipelines. The workshop will feature variant-calling as an example, but the concepts and tools can be applied to nearly any analysis.

Pre-requisites: Basic familiarity with R. Installations of recent versions of R, RStudio, conda, and docker.

Duration: 2 hours

Time/Date: June 30, 2022 at 8:30 PM BST

Who is this for?

Anybody interested in maintaining bioinformatics pipelines with R. There are many pipeline tools available, but I can't tell you which is best for your project. For example, if you mostly do things in python, snakemake may be a better alternative, etc.

This workshop is primarily intended for people who already use R and want to use it to construct and maintain bioinformatics pipelines.

Format

The workshop is split into two parts:

• Part I will introduce the {targets} R package and demonstrate its basic usage.
• Part II will show how to use {targets} in combination with docker and conda to orchestrate bioinformatics workflows.

Resources

• Slides
• Code repository for variant calling workflow using {targets}
• Data Carpentry "Data Wrangling and Processing for Genomics" workshop, basis for the {targets} variant calling workflow
• Blog post describing these methods
• Collaborative notes

Objectives

By the end of the workshop, participants will be able to: - Use basic functions of the {targets} R package - Write wrapper functions calling programs to run in docker from R - Use the {targets} R package to construct bioinformatics pipelines

Not covered

This workshop will not include: - Details about docker - Details about R - Thorough explanation of variant calling

Contributing :hearts:

• If you like it, leave your star in this project :star2:
• If you would like to complain/suggest/contribute to this project, feel free to open a issue :heart_decoration:
• Please follow our contributing guidelines.

Citation

If you use any of the materials of this lesson, please cite as:

Nitta, J.H. 2022. "Modular, reproducible bioinformatics workflows with the targets R package" https://github.com/ISCB-Academy/bioinfo-targets

License

This work is licensed under a Creative Commons Attribution 4.0 International License.