data-provenance skillA
data-provenance is agent-read markdown (skill) from ammawla/encode-toolkit: 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 .
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
# Exact Provenance Tracking and Methods Writing ## When to Use - User wants to track the full analysis chain from ENCODE download through processing to publication figure - User asks about "provenance", "reproducibility", "methods section", or "analysis log" - User needs to log derived files with their processing parameters for audit trail - User wants to auto-generate publication-ready methods text from logged analysis steps - Example queries: "log my peak calling step", "generate a methods section from my analysis", "show the provenance chain for this figure" Track every operation on ENCODE data with exact tool versions, reference files, scripts, parameters, and timestamps to enable publication-ready methods sections. ## Scientific Rationale **The question**: "What exactly was done to this data, and can someone else reproduce it identically?" …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/data-provenance@git:20260920.6050003mdr add ammawla/encode-toolkit/data-provenance@sha256:4d0e3d812cd15f47Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_6ssxqiysztoaix7b)
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Versions
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 26,652 B | A | view · diff |
| git:20260920.992a807 | 2026-09-20 | 992a807 | 25,112 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 25,103 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (26652 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
ammawla/encode-toolkit · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_6ssxqiysztoaix7b GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/data-provenance GET https://markdownregistry.com/api/v1/blob/4d0e3d812cd15f4715194eb1462a76ba90bf567c9412852c132c8cc5cac38457
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