bio-reads-qc-mapping SKILL.md skillA
bio-reads-qc-mapping from fmschulz/omics-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fmschulz/omics-skills/bio-reads-qc-mapping@git:20261001.bf5afd6Pins git:20261001.bf5afd6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fmschulz/omics-skills
- Path
skills/bio-reads-qc-mapping/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- Jul 11, 2026
- Size
- 6,869 bytes
- Repository stars
- 11
- License
- MIT
QC, trim, and map short or long reads with a restartable driver. Use when processing raw FASTQ, removing adapters or contaminants, or computing mapping and coverage statistics.
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
# Bio Reads QC Mapping
Validate a read sample sheet, run read QC and trimming, and map reads to an optional reference with a restartable driver.
## Instructions
Tool guides and versions: [docs/README.md](docs/README.md).
1. Validate `sample_sheet.tsv` against `schemas/sample-sheet.schema.json` and inspect the plan before running anything:
```bash
uv run --script skills/bio-reads-qc-mapping/scripts/run_reads_qc_mapping.py \
sample_sheet.tsv --out results/bio-reads-qc-mapping --threads 4
# Inspect run_manifest.json, then execute the same plan on a compute node:
uv run --script skills/bio-reads-qc-mapping/scripts/run_reads_qc_mapping.py \
sample_sheet.tsv --out results/bio-reads-qc-mapping --threads 16 --execute
```
`read_type` must be `paired_short`, `single_short`, or `long`. Mapping runs only for rows with a non-empty `reference`; a missing reference is not a mapping failure. The driver reuses a stage only when its declared outputs are non-empty and the stage's `.done` marker exists. Run `--execute` through the scheduler (`sbatch`) for real data, not on a login node.
2. Know what the driver runs, and adapt the plan when the defaults do not fit:
…Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-reads-qc-mapping@sha256:29b1dc542275c267The line at the top of this page pins the label git:20261001.bf5afd6, 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_52jpenz44rtnru6n)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jul 11, 2026 and Oct 1, 2026, about one every 16 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261001.bf5afd6 latest | 2026-10-01 | bf5afd6 | 6,869 B | A | view · diff |
| git:20260905.3e49039 | 2026-09-05 | 3e49039 | 6,020 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 5,690 B | A | view · diff |
| git:20260825.bd47e68 | 2026-08-25 | bd47e68 | 6,084 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 5,998 B | A | view · diff |
| git:20260711.5ae6f6f | 2026-07-11 | 5ae6f6f | 5,098 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 (6869 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
fmschulz/omics-skills · 11 stars · license MIT · pushed 2026-10-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_52jpenz44rtnru6n GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-reads-qc-mapping GET https://markdownregistry.com/api/v1/blob/29b1dc542275c26784c469cef442022d00a97ea9cc2e0560ea852e736f652369
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.