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