Conciseness

The body is lean and assumes competence — interpretation rules and input checklists are genuine domain knowledge, with no basic-concept padding — but there is minor redundancy between the four runner invocations in 'Local Execution' and the direct-tool commands in 'Kickoff Pattern' that could be trimmed.

Actionability

Fully executable, copy-paste-ready commands with concrete flags ('--trim-mode cutadapt --adapter-r1 AGATCGGAAGAGC', '--sample-sheet', '-t 4') covering the common cases: QC-only, single paired sample, optional trimming, and explicit adapters.

Workflow Clarity

A clear sequence (Preflight → Local Execution → Interpretation Rules → Output Review) with most checkpoints present ('performs pre-execution validation', 'verify R1/R2 file counts and read-name pairing', 'Do not overwrite input FASTQs'), but there is no explicit error-recovery loop describing what to do when pre-execution validation fails.

Progressive Disclosure

No bundle files exist and the body has clean, well-labeled sections with no nested or buried references; the minor gap is that the four runner command variants could be consolidated or moved to a reference file. The under-50-line exception for a 5 does not apply to this ~120-line body.

Specificity

The description lists multiple concrete, named actions covering the full domain scope — 'Validate FASTQ inputs', 'run local FastQC/MultiQC QC', 'interpret QC signals', and 'optionally execute fastp or Cutadapt trimming branches' — plus an explicit safety constraint ('without overwriting raw reads'), matching the comprehensive-coverage anchor rather than the minor-gaps anchor.

Completeness

The 'what' is explicit and concrete, but there is no 'Use when…' clause or any equivalent trigger guidance, which caps completeness at 3 per the judging guideline.

Trigger Term Quality

Natural user terms are well covered ('FASTQ', 'QC', 'FastQC', 'MultiQC', 'fastp', 'Cutadapt', 'trimming', 'raw reads'), but common variations and synonyms are absent — no '.fastq'/.fq' file extensions, no 'quality control' or 'adapter trimming' phrasing — so it falls short of the comprehensive-synonym anchor.

Distinctiveness Conflict Risk

A clear niche (FASTQ quality control and trimming) with distinct tool-name triggers (FastQC, MultiQC, fastp, Cutadapt) and minimal overlap risk with other skills.