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 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 --no-project python 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 --no-project python 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 is scheduled only for rows with a non-empty `reference`; a missing reference is not a mapping failure. 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` v0.2.1 when selecting reads for assembly. Use `Pychopper` for full-length cDNA. Treat `Porechop_ABI` as a targeted legacy/fallback adapter-discovery tool, and record why it is needed. - For very large ONT FASTQ inputs, do not burn the first full read pass on raw `gzip -t` or raw `seqkit sta