What problem does it solve? Writing an accurate Methods section requires manually tracking which tools, versions, data sources, and parameters were used in an analysis — information that is easy to forget or reconstruct incorrectly. This Skill automates the mechanical extraction of that information from lockfiles and provenance sidecars so the Methods paragraph is grounded in the actual analysis. ## Core Features & Use Cases - Lockfile scanning: Parses requirements.txt, renv.lock, conda environment.yaml, and pyproject.toml to extract tool names, versions, and package sources (PyPI, CRAN, Bioconductor, conda). - Provenance extraction: Reads *.meta.json sidecars to surface sha256 hashes, download dates, source URLs, DOIs, and data versions for each artifact. - Workflow and runtime detection: Finds Snakemake, Nextflow, WDL, and CWL workflow files plus R and Python runtime versions. - Use Case: After finishing a differential expression analysis, run the scanner on the project directory and ask Claude to draft the Methods paragraph — it produces text citing DESeq2 v1.40.2 in R 4.3.2, the GOA download date, and the DOI, ready for the manuscript. ## Quick Start Ask Claude to draft a Methods section for your analysis directory, and it will run scripts/scan.py on that directory and write the paragraph from the resulting JSON.
