pipeline-dnaseseq SKILL.md skillA
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
pipeline-dnaseseq from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/pipeline-dnaseseq@git:20260920.6050003Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
skills/pipeline-dnaseseq/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Sep 20, 2026
- Size
- 24,789 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing DNase-seq data, calling DNase hypersensitive sites, performing footprinting analysis. Trigger on: DNase-seq pipeline, DNase hypersensitive, DHS, Hotspot2, footprinting, DNase I, chromatin accessibility DNase.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# ENCODE DNase-seq Pipeline: FASTQ to Hotspots and Footprints
## When to Use
- User wants to run a DNase-seq processing pipeline from FASTQ to hotspots and footprints
- User asks about "DNase-seq pipeline", "DNase hypersensitive sites", "Hotspot2", "footprinting", or "DHS"
- User needs to process DNase-seq data for chromatin accessibility and TF footprint analysis
- Example queries: "process my DNase-seq FASTQs", "call DNase hypersensitive sites", "run footprinting analysis on DNase-seq"
Execute the ENCODE DNase-seq pipeline for chromatin accessibility profiling,
producing DNase hypersensitive sites (DHSs) via Hotspot2 and transcription
factor footprints.
## Pipeline Overview
```
FASTQ -> Trim -> BWA-MEM align -> Filter/dedup -> Hotspot2 -> DHS peaks
| |
Signal track Footprinting (HINT)
```
### ENCODE Repository
- **GitHub**: `ENCODE-DCC/dnase-seq-pipeline`
- **Container**: built from `scripts/Dockerfile` in this skill (`docker build -t encode-toolkit/pipeline-dnaseseq:1.0.0 scripts/`); override with `--container`
- **WDL**: Available for Cromwell execution
…Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-dnaseseq@sha256:87f0a86d92b98cfcThe line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_yfuipg53efjaa6iy)
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Versions
The registry has recorded 5 versions of this file, all committed on Sep 20, 2026.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 24,789 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 22,806 B | A | view · diff |
| git:20260920.92639e7 | 2026-09-20 | 92639e7 | 17,139 B | A | view · diff |
| git:20260920.bc6cada | 2026-09-20 | bc6cada | 16,460 B | A | view · diff |
| git:20260920.3246884 | 2026-09-20 | 3246884 | 16,460 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 (24789 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 · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_yfuipg53efjaa6iy GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-dnaseseq GET https://markdownregistry.com/api/v1/blob/87f0a86d92b98cfcba43e2a188d8385ae05875ae312d7e3f878f8df6eca029de
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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