pipeline-cutandrun skillA
pipeline-cutandrun is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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 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@git:20260920.6050003mdr add ammawla/encode-toolkit/pipeline-cutandrun@sha256:b37ebef70424dc0fPin 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_vzkegxes5bypbl2s)
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Versions
| 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 |
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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vzkegxes5bypbl2s GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-cutandrun GET https://markdownregistry.com/api/v1/blob/b37ebef70424dc0f4f4e21ee51c66d19e361ea33c4805c7117c93a9959cf191f
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