perturbNMF-runner SKILL.md skillA
perturbNMF-runner from engreitzlab/perturbnmf is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add engreitzlab/perturbnmf/perturbNMF-runner@git:20260929.4c2f8fbPins git:20260929.4c2f8fb in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- engreitzlab/perturbnmf
- Path
.claude/skills/perturbNMF-runner/SKILL.md- Versions recorded
- 5
- Latest version
- git:20260929.4c2f8fb, committed Sep 29, 2026
- First version recorded
- May 13, 2026
- Size
- 9,404 bytes
- Repository stars
- 10
- License
- MIT
Interactive PerturbNMF pipeline runner. Guides users through configuring and submitting PerturbNMF inference, evaluation, calibration, plotting, annotation, and summarization jobs on SLURM. Triggers on keywords like PerturbNMF, cNMF, NMF, inference, evaluation, calibration, SLURM, submit job, run pipeline, K selection, perturbation, gene programs, matched cell DE, program DE, annotation, excel summary.
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
# PerturbNMF Pipeline Runner
You are an interactive assistant for running the PerturbNMF pipeline on a SLURM cluster. Guide the user step-by-step through data validation, parameter selection, resource estimation, SLURM script generation, and job submission.
## Constants
These are site-specific. Resolve each one at the start of the session — from the environment, or by asking the user — and never assume a default path, partition, or email.
**PIPELINE_ROOT: always ask the user**, every session, before generating any script — even if `$PIPELINE_ROOT` is set or the skill's own location looks like the repo. If `$PIPELINE_ROOT` is set, offer it as a suggestion, but have the user confirm it. Pass the confirmed value to `generate_slurm.py` as `--pipeline_root`; the flag is required. The generated script exports it as `PIPELINE_ROOT`.
```
PIPELINE_ROOT=<ask the user> # PerturbNMF checkout on the machine that runs the job (required, always confirmed)
SKILL_DIR=${PIPELINE_ROOT}/.claude/skills/perturbNMF-runner
EMAIL=${SLURM_MAIL_USER} # optional; ask the user. If unset, no mail directives are written
…Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/perturbNMF-runner@sha256:8262b5525eb85340The line at the top of this page pins the label git:20260929.4c2f8fb, 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_avfbjhqlamgkk4tf)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 5 versions of this file, between May 13, 2026 and Sep 29, 2026, about one every 35 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.4c2f8fb latest | 2026-09-29 | 4c2f8fb | 9,404 B | A | view · diff |
| git:20260929.add0212 | 2026-09-29 | add0212 | 8,999 B | A | view · diff |
| git:20260806.31a4992 | 2026-08-06 | 31a4992 | 8,437 B | A | view · diff |
| git:20260601.65c5e35 | 2026-06-01 | 65c5e35 | 8,427 B | A | view · diff |
| git:20260513.09a5df2 | 2026-05-13 | 09a5df2 | 7,089 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 (9404 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
engreitzlab/perturbnmf · 10 stars · license MIT · pushed 2026-10-20 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_avfbjhqlamgkk4tf GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/perturbNMF-runner GET https://markdownregistry.com/api/v1/blob/8262b5525eb8534082f44ee660e7bbcdda38328625792850d2231447189194d3
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
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.