Individual skill

data-provenance

Track exact provenance for every operation on ENCODE data — tool versions, reference files, scripts, parameters, and timestamps — to enable publication-ready methods writing. Use when the user processes ENCODE files, runs any bioinformatics tool, creates filtered/merged datasets, runs pipelines, performs liftover, uses R/Python/Bash for analysis, or needs to document their analysis chain for reproducibility and publication. Also use when the user says "write me methods" to auto-generate methods sections from the provenance log. This skill implements comprehensive provenance documentation: every tool, every version, every reference file, every parameter, every accession — no shortcuts. Use this skill for ANY processing step, ANY file transformation, ANY analysis operation on ENCODE data.

plugin/skills/data-provenance/SKILL.md

Source commit 36836c8725fd4d20d9c851ce314f5151aea5f57c

What was checked

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Yes

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Yes

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No

Observed behavior

Instructions only

Last checked

Nov 6, 2026

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