pipeline-cutandrun 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-cutandrun 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-cutandrun@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-cutandrun/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 8, 2026
- Size
- 25,910 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing CUT&RUN or CUT&Tag data, an alternative to ChIP-seq with lower background. Trigger on: CUT&RUN pipeline, CUT&Tag, SEACR, Henikoff, targeted chromatin, pA-MNase, process CUT&RUN.
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 CUT&RUN Pipeline: FASTQ to Peaks and Signal Tracks
## When to Use
- User wants to run a CUT&RUN or CUT&Tag processing pipeline from FASTQ to peaks
- User asks about "CUT&RUN pipeline", "CUT&Tag", "SEACR", "spike-in normalization", or "targeted chromatin"
- User needs to process CUT&RUN/CUT&Tag data with spike-in calibration and SEACR peak calling
- Example queries: "process my CUT&RUN FASTQs", "run SEACR on CUT&Tag data", "normalize CUT&RUN with spike-in controls"
Execute the CUT&RUN/CUT&Tag processing pipeline for targeted chromatin profiling,
producing peak calls with SEACR and spike-in normalized signal tracks.
## Pipeline Overview
```
FASTQ
|-> FastQC (raw reads)
+-> Trim Galore -> Bowtie2 (genome) -> {sample}.sorted.bam
|
|-> unmapped read pairs -> Bowtie2 (spike-in) -> counts -> scale_factors.txt
| |
+-> filter (MAPQ 10, proper pairs) -> Picard MarkDuplicates |
(removed) -> blacklist filter -> {sample}.filtered.bam |
|-> fragment BED -> fragment bedGraph -> SEACR peaks |
…Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-cutandrun@sha256:b37ebef70424dc0fThe 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_wqvma4r6gktysx6u)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Mar 8, 2026 and Sep 20, 2026, about one every 49 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 25,910 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 24,290 B | A | view · diff |
| git:20260920.767027e | 2026-09-20 | 767027e | 17,891 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 17,171 B | A | view · diff |
| git:20260308.ca46af5 | 2026-03-08 | ca46af5 | 17,182 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 (25910 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_wqvma4r6gktysx6u GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-cutandrun GET https://markdownregistry.com/api/v1/blob/b37ebef70424dc0f4f4e21ee51c66d19e361ea33c4805c7117c93a9959cf191f
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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