method-omics-qc SKILL.md skillA
method-omics-qc from sajor2000/methodsmith is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add sajor2000/methodsmith/method-omics-qc@git:20261016.73e5a37Pins git:20261016.73e5a37 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- sajor2000/methodsmith
- Path
plugins/methodsmith/skills/method-omics-qc/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261016.73e5a37, committed Oct 16, 2026
- Size
- 7,014 bytes
- Repository stars
- 3
- License
- MIT
Runs sequencing and omics QA: FASTQ, BAM/CRAM, VCF, count matrices, methylation arrays, sample swaps, batch confounding. Use when omics data needs QC before analysis.
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
# Bioinformatics Data QA Gate ## Skill Value - **Problem it solves:** Sequencing and omics projects can move into analysis before raw data quality, sample identity, and batch confounding are checked. - **Use when:** The user mentions FASTQ, BAM/CRAM, VCF, RNA-seq, WGS/WES, ATAC-seq, methylation arrays, FastQC, MultiQC, sample swaps, or omics batch effects. - **Output:** A GO/NO-GO omics QA summary with modality-specific checks and blockers for downstream analysis. - **Ask only if:** Only when modality, sample sheet, batch variable, or case/control grouping cannot be inferred. - **Do not do:** Do not run differential expression, association testing, or clinical interpretation. - **Interaction:** Check repo/config/chat evidence first. Ask one decision-changing question at a time; use the current harness's blocking question UI when available, otherwise present numbered choices and wait. The omics counterpart to `method-data-qa`. Sequencing and array data fail in domain-specific ways (low base quality, adapter contamination, sample swaps, batch confounds with condition); this skill runs the right QC for the modality. ## When this skill activates …
Read the whole file at its exact version.
How to install
mdr add sajor2000/methodsmith/method-omics-qc@sha256:b9c9df2dd32bf98dThe line at the top of this page pins the label git:20261016.73e5a37, 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_v6gr4rbj4sdgevep)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Oct 16, 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 (7014 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
sajor2000/methodsmith · 3 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_v6gr4rbj4sdgevep GET https://markdownregistry.com/api/v1/resolve?ref=sajor2000/methodsmith/method-omics-qc GET https://markdownregistry.com/api/v1/blob/b9c9df2dd32bf98d36af5987fb8b70f6220d3b18f6ef744d6cabccfe0d3107c7
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.