bio-reads-qc-mappinglisted

# Bio Reads QC Mapping Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats. ## Instructions Tool guides and versions: [docs/README.md](docs/README.md). 1. Parse and validate `sample_sheet.tsv` against `schemas/sample-sheet.schema.json`. Use the executable driver for both planning and restartable execution: ```bash uv run --script skills/bio-reads-qc-mapping/scripts/run_reads_qc_mapping.py \ sample_sheet.tsv --out results/bio-reads-qc-mapping # Inspect run_manifest.json, then execute the same plan: uv run --script skills/bio-reads-qc-mapping/scripts/run_reads_qc_mapping.py \ sample_sheet.tsv --out results/bio-reads-qc-mapping --execute ``` `read_type` must be `paired_short`, `single_short`, or `long`. Mapping runs only for rows with a non-empty `reference`; a missing reference is not a mapping failure. The driver reuses a stage only when its declared outputs are non-empty and the stage's `.done` marker exists. 2. For short reads: run QC and adapter/quality trimming with `bbduk` or `fastp` v1.3.3+. 3. For long reads: use current basecaller-aware QC first. For ONT, prefer Dorado summaries/trimming during basecalling or demultiplexing when starting from signal/BAM; for FASTQ-only filtering use `chopper` for quality/length/end trimming or `filtlong` v0.3.1 when selecting reads for assembly (v0.3.0 renamed the short-read options to `--short_1` / `--short_2`; see [docs/filtlong.md](docs/filtlong.md)).