pipeline-chipseq skillA
pipeline-chipseq is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
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 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 …
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How to install
mdr add ammawla/encode-toolkit/pipeline-chipseq@git:20260921.ed45b8dmdr add ammawla/encode-toolkit/pipeline-chipseq@sha256:eee6d22cefbfaf38Pin 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_ymusrisuofskuhak)
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Versions
| 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ymusrisuofskuhak 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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