bio-workflow-methods-docwriter SKILL.md skillA
bio-workflow-methods-docwriter 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-workflow-methods-docwriter@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-workflow-methods-docwriter/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- Jul 11, 2026
- Size
- 5,385 bytes
- Repository stars
- 11
- License
- MIT
Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.
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 Workflow Methods Docwriter
Write Methods text and run documentation from real workflow artifacts. Every command, version, and parameter comes from evidence; nothing is inferred.
## Instructions
1. Collect the evidence package listed in [reference/evidence-checklist.md](reference/evidence-checklist.md): launch command, configs, engine version, tool versions or container digests, input checksums or accessions, reference and database versions, QC reports, and the final output list.
2. Build a draft `run_manifest.yaml` with the extractor for the engine:
- Nextflow: `extract_nextflow_run.py` reads `trace.txt` and the `work/` task folders. `--tool-versions` is a JSON mapping of process name to `{"tool": ..., "version": ...}`; `--outputs-manifest` lists one final output path per line.
- Snakemake: `extract_snakemake_run.py` reads a JSONL file with one record per job (`rule`, `status`, `tool`, `version`, `command`, `inputs`, `outputs`). Assemble it from `--printshellcmds` logs and the version records; see `fixtures/snakemake/jobs.jsonl`.
…Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-workflow-methods-docwriter@sha256:44a098660aae466aThe 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_45rl464cwpcnd7xg)
3 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 | 5,385 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 3,352 B | A | view · diff |
| git:20260825.bd47e68 | 2026-08-25 | bd47e68 | 3,089 B | A | view · diff |
| git:20260807.4acaed9 | 2026-08-07 | 4acaed9 | 3,073 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 2,776 B | A | view · diff |
| git:20260711.5ae6f6f | 2026-07-11 | 5ae6f6f | 2,372 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 (5385 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_45rl464cwpcnd7xg GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-workflow-methods-docwriter GET https://markdownregistry.com/api/v1/blob/44a098660aae466a5471c91974436c7c3c662da30877fcba336dff1855b037b8
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.