Resources

A collection of tools, papers, and workflows I've found useful.

Papers

• Classic population genetics papers — curated by the Morrell Lab
• Pollak, Edward. "On the theory of partially inbreeding finite populations. I. Partial selfing." Genetics 117.2 (1987): 353.

Tools & Workflows

RAG CLI

A simple CLI tool for asking questions about papers using retrieval augmented generation.

https://github.com/milesroberts-123/custom-rag-cli/tree/main

Containerizing Snakemake workflows

Generate a Dockerfile from a Snakemake workflow with snakemake --containerize > Dockerfile.

https://github.com/snakemake/snakemake/issues/2602

Snakemake + R Markdown

Embed an R Markdown notebook as a Snakemake rule to generate reports.

https://nbis-reproducible-research.readthedocs.io/en/course_2104/rmarkdown/#r-markdown-and-snakemake