pipeline-hic 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-hic 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-hic@git:20260921.4ba10c6Pins git:20260921.4ba10c6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- ammawla/encode-toolkit
- Path
plugin/skills/pipeline-hic/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260921.4ba10c6, committed Sep 21, 2026
- First version recorded
- Sep 20, 2026
- Size
- 21,796 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, or calling loops. Trigger on: Hi-C pipeline, chromatin conformation, contact matrix, loop calling, TAD detection, Juicer, HiCCUPS, 3D genome.
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 Hi-C Pipeline: FASTQ to Contact Matrices and Loops
## When to Use
- User wants to run a Hi-C processing pipeline from FASTQ to contact matrices and loop calls
- User asks about "Hi-C pipeline", "contact matrix", "loop calling", "Juicer", "HiCCUPS", or "TAD detection"
- User needs to process Hi-C data for 3D genome structure analysis
- Example queries: "process my Hi-C FASTQs", "generate contact matrices from Hi-C", "call chromatin loops with HiCCUPS"
Execute the ENCODE Hi-C pipeline for chromatin conformation capture data,
producing multi-resolution contact matrices and loop calls.
## Pipeline Overview
```
FASTQ -> FastQC (raw reads)
-> bwa mem -SP5M (both mates in one call) -> {sample}.paired.bam
-> pairtools parse -> sort -> dedup -> select UU
|
+-> Juicer pre -> .hic -> HiCCUPS -> loops (BEDPE)
|
+-> cooler cload + zoomify -> .mcool
```
### Not run by this workflow
Adapter trimming, TAD calling, A/B compartment calling, and every cooltools
analysis are outside this workflow. They are documented as manual, optional
steps only: trimming in `references/01-qc-trimming.md`, distance decay and
…Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-hic@sha256:0181f164858afd5bThe line at the top of this page pins the label git:20260921.4ba10c6, 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_uds6xmvyxdhv2ixj)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between Sep 20, 2026 and Sep 21, 2026, more than one a day.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 21,796 B | A | view · diff |
| git:20260921.ed45b8d | 2026-09-21 | ed45b8d | 21,751 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 21,704 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 20,054 B | A | view · diff |
| git:20260920.bc6cada | 2026-09-20 | bc6cada | 15,575 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 (21796 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_uds6xmvyxdhv2ixj GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-hic GET https://markdownregistry.com/api/v1/blob/0181f164858afd5beb3fe5b8f665e132c86f8013d688455c1a6476991bb4c0ff
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.
More from ammawla/encode-toolkit
Every file in ammawla/encode-toolkit