pipeline-dnaseseq skillA
pipeline-dnaseseq is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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
# 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@git:20260920.6050003mdr add ammawla/encode-toolkit/pipeline-dnaseseq@sha256:87f0a86d92b98cfcPin 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_tcy677l4u5tvfxt2)
1 badge views in 30 days
Versions
| 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_tcy677l4u5tvfxt2 GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-dnaseseq GET https://markdownregistry.com/api/v1/blob/87f0a86d92b98cfcba43e2a188d8385ae05875ae312d7e3f878f8df6eca029de
Your agent 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.