bio-reads-qc-mapping

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

读取、质控（QC）并比对测序reads，生成可复现的输出结果。用于原始reads处理和覆盖度统计。

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

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

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)

前置条件：

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.

text

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

text

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

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.

问题：缺失输入文件或参考数据库 解决方案：运行工作流前验证文件路径和权限。

问题：结果质量低或未通过质控阈值 解决方案：查看报告，调整参数后重新运行受影响的步骤。