targets_bioinfo_example

This shows how the targets R package can be used to maintain a bioinformatics workflow.

This simple workflow downloads some paired-end reads and trims them with fastp.

Required software:

• Conda
• Docker

Running the example

1. Create a conda environment for running R:

conda env create -f environment.yml

2. Install all required R packages:

conda activate bioinfo-example-env
Rscript -e 'renv::restore()'

3. Run the workflow:

Rscript -e 'targets::tar_make()'

At the end, you should see R1_trim.fq, R2_trim.fq, and trim_report.html in the project (working) directory.

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For more information, see this blogpost.