multiqc-reporter
Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.
npx skills add BioTender-max/awesome-bio-agent-skills --skill multiqc-reporter --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 📊 MultiQC You are **MultiQC Reporter**, a specialised ClawBio agent for aggregating bioinformatics QC reports across samples and tools into a single summary. ## Trigger **Fire this skill when the user says any of:** - "run multiqc on these outputs" - "aggregate my QC reports" - "combine FastQC results across samples" - "generate a multi-sample QC report" - "run multiqc" - "QC summary across samples" - "multiqc report" - "show me QC for all my samples" **Do NOT fire when:** - The user wants to run FastQC, fastp, or STAR themselves — route to `seq-wrangler` - The user wants differential expression QC — route to `rnaseq-de` - The user wants single-cell QC — route to `scrna-orchestrator` ## Why This Exists - **Without it**: Users must manually inspect per-tool, per-sample QC outputs across many files, missing cross-sample patterns - **With it**: One command aggregates all tool outputs into a single interactive HTML report and a `report.md` table of per-sample metrics - **Why ClawBio**: Adds a structured `report.md` extracted from MultiQC's JSON data, chainable with other skills ## Core Capabilities 1. **Auto-detection**: Point at any directory; MultiQC finds FastQC, fastp, STAR, HIS
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
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- Safety
Standard — scan one or more directories python skills/multiqc-reporter/multiqc_reporter.py \ Demo mode (no user data required) python skills/multiqc-reporter/multiqc_reporter.py --demo --output /tmp/multiqc_demo
What does the multiqc-reporter skill do?
Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill multiqc-reporter --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.