Bio Reads QC Mapping

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

Instructions

1. Parse sample sheet and validate inputs.
2. For short reads: Run QC/trimming (bbduk).
3. For long reads: Trim adapters (Porechop) and filter by quality/length (Filtlong).
4. Map reads (bbmap or minimap2) and generate coverage tables.

Quick Reference

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See docs/README.md.
References	- See ../bio-skills-references.md

Input Requirements

Prerequisites:

• Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
• Sample sheet and reads are available. Inputs:
• sample_sheet.tsv
• reads/*.fastq.gz
• reference.fasta (optional)

Output

• results/bio-reads-qc-mapping/trimmed_reads/
• results/bio-reads-qc-mapping/qc_reports/
• results/bio-reads-qc-mapping/mapping_stats.tsv
• results/bio-reads-qc-mapping/coverage.tsv
• results/bio-reads-qc-mapping/logs/

Quality Gates

• Post-QC read count sanity checks pass.
• Mapping rate meets project thresholds.
• On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
• Validate sample sheet schema and FASTQ integrity.

Examples

Example 1: Expected input layout

sample_sheet.tsv
reads/*.fastq.gz
reference.fasta (optional)

Troubleshooting

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.