New: 98,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Multiqc Reporter

by ClawBio in ClawBio/ClawBio

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.

MITAuto-check passedResearch & Science

Install Multiqc Reporter

skills CLI
$ npx skills add ClawBio/ClawBio --skill multiqc-reporter -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio multiqc-reporter --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/multiqc-reporter .claude/skills/multiqc-reporter && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
multiqc-reporter
GitHub stars
1.2k
Used in
1 other repo
Token cost
~2.4k tokens
SKILL.md length
816 words
Files
4
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

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.

  • Works in 3 steps: Auto-detection: Point at any directory;… → Markdown table: Reads… → Demo mode: --demo runs without user data…
  • Tasks that involve Bioinformatics
  • SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 14 more sections
  • Runs Python scripts from its folder; calls python and pip

What it does

Multiqc Reporter is an agent skill from ClawBio/ClawBio. 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.

Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `multiqc_reporter.py`, `tests/__init__.py` and `tests/test_multiqc_reporter.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “Use the multiqc-reporter skill to aggregate QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a…”
  • “/multiqc-reporter”

Requirements

  • Python 3

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

  1. Auto-detection: Point at any directory; MultiQC finds FastQC, fastp, STAR, HISAT2, Picard, samtools stats, Salmon, featureCounts, and 100+…
  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

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • doi.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Multiqc Reporter loads about 2.4k tokens when it runs. Until then it costs about 54 tokens; SKILL.md has 816 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~54
When it runs · the whole SKILL.md, loaded when a task matches
~2.4k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 816 words, ~2,403 tokens.

Download SKILL.mdSave it as .claude/skills/multiqc-reporter/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
multiqc-reporter
description
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.
license
MIT
metadata.version
0.1.0
metadata.author
Cameron Lloyd
metadata.domain
genomics
metadata.tags
qc, fastqc, multiqc, sequencing, alignment, rna-seq, wgs, wes, aggregation

📊 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, 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

FormatExtensionNotes
FastQC outputfastqc_data.txt or *_fastqc.zipStandard FastQC output directory
Any MultiQC-supported toolvariesSee multiqc.info for full list of 100+ tools

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

bash
# 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

markdown
# 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
Show full SKILL.md (361 more words)Show less

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

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files in skills/multiqc-reporter of ClawBio/ClawBio.

  • SKILL.md
  • multiqc_reporter.py
  • tests/__init__.py
  • tests/test_multiqc_reporter.py

Open the folder on GitHubat commit dece754

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Multiqc Reporter next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Multiqc Reporter compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Multiqc Reporter this skillClawBio/ClawBio1.2k1 repos~2.4kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

Similar skills

  • Alphagenome Single Variant Analysis

    google-deepmind/science-skills

    Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.

    3.2k GitHub starsUsed in 2 repos~3k tokens
    Research & ScienceAuto-check: notes

  • 13C Metabolic Flux Analysis

    K-Dense-AI/scientific-agent-skills

    Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.

    48k GitHub starsUsed in 1 repo~3.2k tokens
    Research & ScienceAuto-check passed

  • Clinvar Database

    google-deepmind/science-skills

    A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…

    3.2k GitHub starsUsed in 2 repos~3.9k tokens
    Research & ScienceAuto-check: notes

  • Metabolic Study Planner

    aiming-lab/AutoResearchClaw

    Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.

    15k GitHub stars~1.9k tokensUpdated 1 mo ago
    Research & ScienceAuto-check passed

  • Dbsnp Database

    google-deepmind/science-skills

    A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.

    3.2k GitHub starsUsed in 2 repos~3.4k tokens
    Research & ScienceAuto-check: notes

  • MFA Pipeline Orchestrator

    aiming-lab/AutoResearchClaw

    Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.

    15k GitHub stars~923 tokensUpdated 1 mo ago
    Research & ScienceAuto-check passed

More from ClawBio/ClawBio

All 104 skills in this repo

  • Eqtl Catalogue Region Fetch

    ClawBio/ClawBio

    Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP.

    1.2k GitHub starsUsed in 1 repo~4.7k tokens
    Auto-check passed

  • Xena Tcga Gene Query

    ClawBio/ClawBio

    Query TCGA tumor biology through the ucscxenatoolspy API. An agent skill from ClawBio/ClawBio.

    1.2k GitHub stars~4.7k tokensUpdated yesterday
    Auto-check passed

  • Gwas Catalog Region Fetch

    ClawBio/ClawBio

    Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP.

    1.2k GitHub starsUsed in 1 repo~3.5k tokens
    Auto-check passed

  • Dnasp

    ClawBio/ClawBio

    Population genetics of pre-aligned DNA sequences or multi-sample VCFs using selected DnaSP 6 methods.

    1.2k GitHub stars~5.1k tokensUpdated yesterday
    Auto-check passed

  • Ld 1000g Region Compute

    ClawBio/ClawBio

    Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified.

    1.2k GitHub stars~3.9k tokensUpdated yesterday
    Auto-check passed

  • Ncbi Datasets

    ClawBio/ClawBio

    Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

    1.2k GitHub starsUsed in 1 repo~2.8k tokens
    Auto-check passed

Categories

Questions about Multiqc Reporter

What does Multiqc Reporter 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. Multiqc Reporter is an agent skill from ClawBio/ClawBio.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.

When should I use Multiqc Reporter?

Multiqc Reporter fits situations like: tasks that involve Bioinformatics.

How do I install Multiqc Reporter in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill multiqc-reporter -a claude-code`. Or copy the skill folder (skills/multiqc-reporter in ClawBio/ClawBio) into .claude/skills/multiqc-reporter in your project. Claude Code loads it when a task matches its description.

How do I install Multiqc Reporter in Codex?

Run `npx skills add ClawBio/ClawBio --skill multiqc-reporter -a codex`. Or copy the skill folder (skills/multiqc-reporter in ClawBio/ClawBio) into .agents/skills/multiqc-reporter in your project. Codex loads it when a task matches its description.

Can I use Multiqc Reporter in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill multiqc-reporter -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/multiqc-reporter, .gemini/skills/multiqc-reporter, .github/skills/multiqc-reporter and .opencode/skills/multiqc-reporter in your project.

What does Multiqc Reporter need to run?

Going by SKILL.md and its folder, Multiqc Reporter needs Python for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3.

Does Multiqc Reporter access the network?

SKILL.md names 1 domain. As links in the text: doi.org. This is read from the text; nothing was executed.

Is Multiqc Reporter safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Multiqc Reporter use?

Multiqc Reporter is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Multiqc Reporter use?

About 2.4k tokens (SKILL.md is roughly 9.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Multiqc Reporter?

Skills that share tags, products or a category with Multiqc Reporter: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Multiqc Reporter?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.