pipeline-rnaseq SKILL.md skillA
pipeline-rnaseq 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-rnaseq@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
skills/pipeline-rnaseq/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260921.4ba10c6, committed Sep 21, 2026
- First version recorded
- Mar 12, 2026
- Size
- 28,885 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.
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 RNA-seq Pipeline ## When to Use - User wants to run an RNA-seq processing pipeline from FASTQ to gene quantification - User asks about "RNA-seq pipeline", "STAR alignment", "RSEM", "gene expression quantification", or "Kallisto" - User needs to process bulk RNA-seq data with ENCODE-standard 2-pass STAR alignment - Example queries: "process my RNA-seq FASTQs", "quantify gene expression from RNA-seq", "run STAR and RSEM on my data" Execute the ENCODE RNA-seq processing pipeline from raw FASTQ files through splice-aware alignment, gene/transcript quantification, and strand-specific signal track generation. This skill provides a complete Nextflow DSL2 implementation following ENCODE uniform analysis standards. ## Overview RNA-seq measures transcriptome-wide gene expression by sequencing cDNA derived from cellular RNA. The ENCODE pipeline processes RNA-seq data through quality control, splice-aware alignment with STAR (2-pass mode), gene and transcript quantification with RSEM, optional fast pseudoalignment with Kallisto, and generation of strand-specific signal tracks as bigWig files. Key design decisions: STAR 2-pass mode for maximum splice junction sensitivity, RSEM …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/pipeline-rnaseq@sha256:c21c680c6b81ffa3The 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_gnkmwxpexn5c2mpy)
3 badge image fetches in 30 days. What the badge shows.
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:20260921.4ba10c6 latest | 2026-09-21 | 4ba10c6 | 28,885 B | A | view · diff |
| git:20260920.6050003 | 2026-09-20 | 6050003 | 28,879 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 27,118 B | A | view · diff |
| git:20260321.d9029d0 | 2026-03-21 | d9029d0 | 19,939 B | A | view · diff |
| git:20260312.be32706 | 2026-03-12 | be32706 | 19,914 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 (28885 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_gnkmwxpexn5c2mpy GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/pipeline-rnaseq GET https://markdownregistry.com/api/v1/blob/c21c680c6b81ffa31c9a0ca3939832f0c210b27242e3ad0aff487ed4197e7fa8
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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.
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