Multiqc Reporter

Core Capabilities

1. Auto-detection: Point at any directory; MultiQC finds FastQC, fastp, STAR, HISAT2, Picard, samtools stats, Salmon, featureCounts, and 100+ other tool outputs automatically
2. Markdown table: Reads multiqc_data/multiqc_data.json for per-sample metrics and renders them in report.md
3. Demo mode: --demo runs without user data — generates synthetic FastQC output for 3 samples so MultiQC renders its full plot suite

Scope

One skill, one task. This skill aggregates existing QC outputs via MultiQC. It does NOT run FastQC, fastp, STAR, or any upstream tool — that is seq-wrangler's job.

Input Formats

Workflow

When the user asks to aggregate QC reports:

1. Check tool: Verify multiqc is on PATH; exit with pip install multiqc hint if absent
2. Validate: Confirm all --input directories exist
3. Run: Execute multiqc <dirs> --outdir <output> (MultiQC defaults)
4. Parse: Read multiqc_data/multiqc_data.json for per-sample metrics
5. Report: Write report.md with run metadata, per-sample QC table, and disclaimer
6. Reproducibility: Write reproducibility/commands.sh, environment.yml, and checksums.sha256

CLI Reference

# Standard — scan one or more directories
python skills/multiqc-reporter/multiqc_reporter.py \
  --input <dir> [<dir2> ...] --output <report_dir>

# Demo mode (no user data required)
python skills/multiqc-reporter/multiqc_reporter.py --demo --output /tmp/multiqc_demo

Algorithm / Methodology

1. Shell out to multiqc CLI with --outdir only (default MultiQC behaviour)
2. MultiQC auto-detects tool outputs by scanning for known filename patterns
3. Parse multiqc_data/multiqc_data.json (report_general_stats_data): flatten {tool: {sample: metrics}} → {sample: {metric: value}}
4. Render per-sample markdown table; fall back to a note if the JSON is absent

Example Queries

• "Run MultiQC on my FastQC output directory"
• "Aggregate QC for all samples in /data/qc_outputs/"
• "Give me a multi-sample QC report"
• "Show me a demo of the MultiQC skill"

Example Output

# MultiQC Report

**Date**: 2026-04-13 10:32 UTC
**Input directories**: /data/fastqc_out

## Per-Sample QC

| Sample | percent_duplicates | percent_gc | total_sequences |
|--------|--------------------|------------|-----------------|
| SAMPLE_01 | 5.5 | 49 | 1000000 |
| SAMPLE_02 | 15.0 | 50 | 920000 |
| SAMPLE_03 | 7.5 | 48 | 880000 |

## Outputs

- `multiqc_report.html` — interactive HTML report
- `multiqc_data/` — raw data files

## Reproducibility

- `reproducibility/commands.sh` — replay this ClawBio MultiQC run
- `reproducibility/environment.yml` — suggested conda environment
- `reproducibility/checksums.sha256` — key outputs

---

*ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.*

Output Structure

output_dir/
├── report.md                        # ClawBio markdown summary
├── multiqc_report.html              # Standard MultiQC HTML
├── multiqc_data/
│   ├── multiqc_data.json            # Structured stats (default MultiQC output)
│   └── ...
├── reproducibility/
│   ├── commands.sh                  # Exact replay command
│   ├── environment.yml              # Suggested env (multiqc via pip)
│   └── checksums.sha256             # Output digests

Dependencies

External binary (not a Python package import):

• multiqc >= 1.20; install with pip install multiqc

Python (repo-local clawbio package for reproducibility helpers):

• subprocess, json, shutil, argparse, tempfile, math
• clawbio.common.reproducibility — commands.sh, environment.yml, checksums.sha256

Gotchas

• You will want to parse tool-specific files directly. Do not. MultiQC's auto-detection handles this; let it do its job. Parsing FastQC text yourself will miss 99 other supported tools.
• report_general_stats_data metric keys are already short (e.g. percent_duplicates, percent_gc) — no further processing needed. If the table looks empty, check that multiqc_data/multiqc_data.json exists and that report_general_stats_data is non-empty.
• --demo creates files in a tempfile.TemporaryDirectory that is deleted after run_multiqc returns. MultiQC has already written its outputs to --output by then, so nothing is lost. Don't move the with block boundary.
• MultiQC exits 0 even if it found no recognised files — it just produces an empty report. The skill does not treat this as an error; the user will see an empty table in report.md and an HTML report noting no modules were found.
• Static PNG/SVG/PDF plots are not produced by this skill — it never passes MultiQC --export. Interactive plots remain in multiqc_report.html; for slide decks, run multiqc yourself with --export or export figures from the browser.

Safety

• Local-first: All processing is local; no data is uploaded
• Disclaimer: Every report.md includes the ClawBio medical disclaimer
• No hallucinated metrics: All values in the table come directly from multiqc_data/multiqc_data.json

Agent Boundary

The agent (LLM) dispatches and explains results. The skill (Python + MultiQC CLI) executes. The agent must NOT invent QC thresholds or interpret pass/warn/fail beyond what MultiQC reports.

Integration with Bio Orchestrator

Trigger conditions: the orchestrator routes here when:

• User mentions "multiqc", "aggregate QC", "multi-sample QC report"
• Output directory from seq-wrangler, rnaseq-de, or scrna-orchestrator is provided alongside a request to summarise QC

Chaining partners:

• seq-wrangler: produces FastQC/fastp/BAM stats directories → feed into multiqc
• rnaseq-de: STAR/HISAT2 alignment logs → feed into multiqc for alignment QC
• scrna-orchestrator: STARsolo per-sample QC dirs → feed into multiqc
• repro-enforcer: folds the reproducibility/ trio into pipeline-wide bundles

Maintenance

• Review cadence: Re-evaluate when MultiQC releases a major version (check multiqc --version)
• Staleness signals: If per-sample tables are empty after a MultiQC upgrade, check whether report_general_stats_data still exists in multiqc_data.json
• Deprecation: Archive to skills/_deprecated/ if MultiQC adds a native ClawBio integration

Citations

• Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics (2016). https://doi.org/10.1093/bioinformatics/btw354