pipeline-atacseq SKILL.md skillA
pipeline-atacseq 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-atacseq@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-atacseq/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 29,249 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute ENCODE ATAC-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. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosome-free fragment selection. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS…
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 ATAC-seq Pipeline ## When to Use - User wants to run an ATAC-seq processing pipeline from FASTQ to peaks and signal tracks - User asks about "ATAC-seq pipeline", "Tn5 shift", "chromatin accessibility pipeline", or "Bowtie2 for ATAC" - User needs to process ATAC-seq data with proper Tn5 insertion site correction - Example queries: "process my ATAC-seq FASTQs", "run ENCODE ATAC-seq pipeline", "call accessibility peaks from ATAC-seq" Execute the ENCODE ATAC-seq processing pipeline from raw FASTQ files through Tn5 offset correction, peak calling, IDR analysis, and signal track generation. This skill provides a Nextflow DSL2 implementation following ENCODE uniform analysis standards. TSS enrichment scoring is a **manual post-processing step**; the workflow does not compute it (see "Manual QC steps" below and `references/05-qc-metrics.md`). ## Overview ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) uses the Tn5 transposase to probe open chromatin regions. This pipeline processes ATAC-seq data through quality control, alignment with Bowtie2, mitochondrial read removal, duplicate …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-atacseq@sha256:25f7c5ae26ca7d91The 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_garbvboh6wobihsw)
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Versions
The registry has recorded 5 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 48 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260920.6050003 latest | 2026-09-20 | 6050003 | 29,249 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 26,588 B | A | view · diff |
| git:20260920.bc6cada | 2026-09-20 | bc6cada | 18,244 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 18,187 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 18,088 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 (29249 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_garbvboh6wobihsw GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-atacseq GET https://markdownregistry.com/api/v1/blob/25f7c5ae26ca7d91b8c303cd443625a90ccab34a7d708fb6a5d6cc605fccf2ff
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