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Fastqc multiqc read qc starter

Skill ma-compbio-lab/SkillFoundry/skills/genomics/fastqc-multiqc-read-qc-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill fastqc-multiqc-read-qc-starter

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SKILL.md

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FastQC MultiQC Read QC Starter

Use this skill to run a deterministic read-QC pass with FastQC and aggregate the result with MultiQC on a tiny FASTQ example.

What it does

  • Runs FastQC on a local FASTQ input from the repo-managed genomics prefix.
  • Forces the prefix bin/ onto PATH so the bundled java runtime is discoverable.
  • Runs MultiQC over the FastQC output directory and writes a compact JSON summary.

When to use it

  • You need a verified starter for sequencing read quality control.
  • You want a minimal example of how FastQC and MultiQC fit together before adding trimming or alignment.
  • You need deterministic summary fields for smoke tests or downstream demos.

Example

python3 skills/genomics/fastqc-multiqc-read-qc-starter/scripts/run_fastqc_multiqc_read_qc.py \
  --input skills/genomics/fastqc-multiqc-read-qc-starter/examples/toy_reads.fastq \
  --summary-out scratch/genomics/fastqc_multiqc_summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/genomics/fastqc-multiqc-read-qc-starter/tests -p 'test_*.py'
  • Expected summary: total_sequences == 4, gc_percent == 50, and multiqc_sample_count == 1

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