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
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.
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.
- 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
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
This workshop will not include:
- Details about docker
- Details about R
- Thorough explanation of variant calling
- If you like it, leave your star in this project 🌟
- If you would like to complain/suggest/contribute to this project, feel free to open a issue 💟
- Please follow our contributing guidelines.
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
This work is licensed under a Creative Commons Attribution 4.0 International License.
