nextflow-development SKILL.md skillA
nextflow-development from nota-america/forgecat-agent-profiles is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nota-america/forgecat-agent-profiles/nextflow-development@git:20260610.c645100Pins git:20260610.c645100 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nota-america/forgecat-agent-profiles
- Path
profiles/anthropics/knowledge-work-plugins/anthropics_knowledge-work-plugins_bio-research/for-codex/.agents/skills/nextflow-development/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260610.c645100, committed Jun 10, 2026
- Size
- 8,898 bytes
- Repository stars
- 93
- License
- Apache-2.0
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on.
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
# nf-core Pipeline Deployment Run nf-core bioinformatics pipelines on local or public sequencing data. **Target users:** Bench scientists and researchers without specialized bioinformatics training who need to run large-scale omics analyses—differential expression, variant calling, or chromatin accessibility analysis. ## Workflow Checklist ``` - [ ] Step 0: Acquire data (if from GEO/SRA) - [ ] Step 1: Environment check (MUST pass) - [ ] Step 2: Select pipeline (confirm with user) - [ ] Step 3: Run test profile (MUST pass) - [ ] Step 4: Create samplesheet - [ ] Step 5: Configure & run (confirm genome with user) - [ ] Step 6: Verify outputs ``` --- ## Step 0: Acquire Data (GEO/SRA Only) **Skip this step if user has local FASTQ files.** For public datasets, fetch from GEO/SRA first. See [references/geo-sra-acquisition.md](references/geo-sra-acquisition.md) for the full workflow. **Quick start:** ```bash # 1. Get study info python scripts/sra_geo_fetch.py info GSE110004 # 2. Download (interactive mode) python scripts/sra_geo_fetch.py download GSE110004 -o ./fastq -i # 3. Generate samplesheet …
Read the whole file at its exact version.
How to install
mdr add nota-america/forgecat-agent-profiles/nextflow-development@sha256:8ea1e9c5976413d0The line at the top of this page pins the label git:20260610.c645100, 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_agpahn6dgo6whrfn)
6 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Jun 10, 2026.
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 (8898 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
nota-america/forgecat-agent-profiles · 93 stars · license Apache-2.0 · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_agpahn6dgo6whrfn GET https://markdownregistry.com/api/v1/resolve?ref=nota-america/forgecat-agent-profiles/nextflow-development GET https://markdownregistry.com/api/v1/blob/8ea1e9c5976413d025e86adbd7a1c3fa4e22d2759f5dcbab60b38d796107cb47
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.
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