pipeline-chipseq SKILL.md skillA
pipeline-chipseq 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-chipseq@git:20260921.ed45b8dPins git:20260921.ed45b8d 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-chipseq/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260921.ed45b8d, committed Sep 21, 2026
- First version recorded
- Mar 12, 2026
- Size
- 29,157 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.
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 ChIP-seq Pipeline ## When to Use - User wants to run a ChIP-seq processing pipeline from FASTQ to peaks and signal tracks - User asks about "ChIP-seq pipeline", "MACS2", "peak calling", "BWA alignment for ChIP", or "IDR" - User needs to process histone or TF ChIP-seq data following ENCODE standards - Example queries: "process my ChIP-seq FASTQs", "run the ENCODE ChIP-seq pipeline", "call peaks from ChIP-seq with MACS2 and IDR" Execute the ENCODE ChIP-seq processing pipeline from raw FASTQ files through peak calling, IDR analysis, and signal track generation. This skill provides a Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview The pipeline processes chromatin immunoprecipitation sequencing data through quality control, adapter trimming, alignment to a reference genome, filtering and duplicate removal, blacklist filtering, peak calling with MACS2, an IDR comparison for every pair of replicates, FRiP calculation, and signal track generation. The same workflow handles transcription factor (TF) ChIP-seq and histone modification ChIP-seq. The peak mode is chosen once per run with `--peak_type narrow|broad`; it applies …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-chipseq@sha256:eee6d22cefbfaf38The line at the top of this page pins the label git:20260921.ed45b8d, 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_larcuv7gy4nzcqgi)
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Versions
The registry has recorded 5 versions of this file, between Mar 12, 2026 and Sep 21, 2026, about one every 48 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260921.ed45b8d latest | 2026-09-21 | ed45b8d | 29,157 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 28,983 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 26,828 B | A | view · diff |
| git:20260920.3246884 | 2026-09-20 | 3246884 | 18,175 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 18,173 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 (29157 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_larcuv7gy4nzcqgi GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-chipseq GET https://markdownregistry.com/api/v1/blob/eee6d22cefbfaf385abc6c32220e0e575be92693e7bded307b4e6859d47e4f5b
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