pacsomatic SKILL.md skillA
pacsomatic from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/pacsomatic@v1.4Pins v1.4 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/pacsomatic/SKILL.md- Versions recorded
- 6
- Latest version
- v1.4, committed Oct 1, 2026
- First version recorded
- Jun 11, 2026
- Size
- 6,477 bytes
- Repository stars
- 56,497
- License
- MIT
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.
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
# pacsomatic ## When to use Use [scripts/run_pacsomatic.py](scripts/run_pacsomatic.py) to prepare one matched PacBio HiFi tumor/normal pair, generate a samplesheet and reproducible launch artifacts, and launch locally or submit the **Nextflow driver** to a scheduler. The pipeline realigns input BAMs; this helper targets unaligned HiFi BAMs and optional PacBio `.pbi` indexes. Do not substitute short reads or treat a BAM filename as evidence of platform, matched identity, or methylation information. The reviewed upstream `dev` commit is `24c84cb371b0339c1d65a4de9451671945e19772`. GitHub had no releases or tags on 2026-10-01, despite the internal manifest saying `1.0.0`. The helper pins that commit by default for `nf-core/pacsomatic`; it does not invent a release tag. This is a source-reviewed development workflow, not a clinically validated assay. See [references/pacsomatic_guide.md](references/pacsomatic_guide.md) for sources and scientific checks. ## Workflow 1. Obtain distinct tumor and normal BAM paths, patient ID, distinct sample IDs, output directory, and exactly one reference mode: `--fasta` or `--genome`. …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/pacsomatic@sha256:5425319387beb296The line at the top of this page pins the label v1.4, 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_anprnvn7e4wxqicd)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jun 11, 2026 and Oct 1, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.4 latest | 2026-10-01 | a92663a | 6,477 B | A | view · diff |
| v1.3 | 2026-09-30 | ce9e6e9 | 5,352 B | A | view · diff |
| v1.2 | 2026-07-28 | 0e45106 | 5,056 B | A | view · diff |
| v1.1 | 2026-07-26 | 2f2022d | 5,056 B | A | view · diff |
| v1.0 | 2026-07-26 | b085e11 | 5,045 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 5,056 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 (6477 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
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_anprnvn7e4wxqicd GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/pacsomatic GET https://markdownregistry.com/api/v1/blob/5425319387beb29684ae5148cba33bd3a6c4306651ba574d47c76a8dc390d45d
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.