Reproducible Bioinformatics Pipelines in R with Capsule

Sravan Koduri

Overview

  • Reproducibility is a core problem in genomics and bioinformatics.
  • Capsule is a new R package that captures code, environment, and tools for full pipeline reproducibility.

The reproducibility problem

  • Typical RNA seq pipeline: FASTQ → alignment → quantification → differential expression.
  • Reproducing later requires the same R packages, external tools, reference genomes, and parameters.

What Capsule provides

  • A “comprehensive reproducibility framework” for R and bioinformatics workflows on CRAN (released Nov 2025).
  • Tracks R session, package versions, external tools reference files, parameters, and hardware.

Starting a Capsule analysis

  • Initializes a registry where Capsule records metadata for this analysis.

    library(Capsule)
    start_capsule(
    analysis_name = "rnaseq_demo",
    registry_dir = ".capsule"
    )

Tracking data and parameters

  • Explicitly records which reference genome and key analysis thresholds were used.

    track_reference_genome(
    fasta = "GRCh38.fa",
    gtf = "gencode.v44.gtf",
    analysis_name = "rnaseq_demo"
    )

    track_params(
    list(alpha = 0.05, lfc_threshold = 1),
    analysis_name = "rnaseq_demo",
    description = "DESeq2 thresholds"
    )

Generating a reproducible script

  • Produces a script plus environment metadata that can be re-run with the same packages and configuration.

    generate_repro_script(
    script_file = "rnaseq_demo_repro.R",
    source_script = "rnaseq_demo.R",
    analysis_name = "rnaseq_demo",
    include_renv = TRUE,
    include_data_check = TRUE,
    include_session_info = TRUE
    )

Workflow manager integration

  • Capsule is designed to integrate with workflow managers like Nextflow, Snakemake, WDL, and CWL.
  • This makes it suitable for real HPC scale genomics pipelines, not just small R scripts.

Why this matters (to me)

  • Genomics projects often need to be rerun months later for reviewers or new data.
  • Capsule eliminates the chance of missing parts of your analysis environment.

Why this matters (to you)

  • Bioinformatics is a fast growing field and it already represents a significant segment of data science job postings.
  • Building reproducible pipelines with tools like Capsule is a marketable skill that can streamline team workflows.

Takeaways

  • Problem: Incomplete documentation makes bioinformatics hard to reproduce.
  • Solution: Capsule, a new CRAN available framework that automates full pipeline reproducibility for R centric workflows.

References

“Capsule.” Comprehensive R Archive Network (CRAN), 10 Nov. 2025, cran.r-project.org/web/packages/Capsule/Capsule.pdf. Accessed 16 Dec. 2025.

“Help for package Capsule.” Comprehensive R Archive Network (CRAN), 5 Nov. 2025, cran.r-project.org/web/packages/Capsule/refman/Capsule.html. Accessed 16 Dec. 2025.