pipeline-atacseq skillA
pipeline-atacseq is agent-read markdown (skill) from ammawla/encode-toolkit: 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 e.
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 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 …
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How to install
mdr add ammawla/encode-toolkit/pipeline-atacseq@git:20260920.6050003mdr add ammawla/encode-toolkit/pipeline-atacseq@sha256:25f7c5ae26ca7d91Pin 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_khiqlc4n3gd45kjp)
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Versions
| 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
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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_khiqlc4n3gd45kjp 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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