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bio-reads-qc-mapping

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Bio Reads QC Mapping

生物测序Reads质控与比对

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。

Instructions

操作步骤

  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.
  1. 解析样本表格并验证输入文件。
  2. 对于短reads：运行质控/修剪（使用bbduk工具）。
  3. 对于长reads：修剪接头序列（使用Porechop）并按质量/长度过滤（使用Filtlong）。
  4. 比对reads（使用bbmap或minimap2）并生成覆盖度表格。

Quick Reference

快速参考

TaskAction
Run workflowFollow the steps in this skill and capture outputs.
Validate inputsConfirm required inputs and reference data exist.
Review outputsInspect reports and QC gates before proceeding.
Tool docsSee 
docs/README.md
.
References- See ../bio-skills-references.md
任务操作
运行工作流遵循本技能中的步骤并保存输出结果。
验证输入确认所需输入文件和参考数据已存在。
检查输出在继续后续步骤前，检查报告和质控阈值。
工具文档查看
docs/README.md
。
参考资料- 查看../bio-skills-references.md

Input Requirements

输入要求

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：
  • 运行环境中已安装所需工具（Pixi/conda/系统级）。所需工具列表请见
    docs/README.md
    。
  • 样本表格和reads文件已准备就绪。 输入文件：
  • sample_sheet.tsv
  • reads/*.fastq.gz
  • reference.fasta（可选）

Output

输出结果

  • 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/
  • 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

质控阈值

  • 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.
  • 质控后reads数量合理性检查通过。
  • 比对率达到项目阈值要求。
  • 若失败：使用替代参数重试；若仍失败，在报告中记录并以非零状态退出。
  • 验证样本表格格式和FASTQ文件完整性。

Examples

示例

Example 1: Expected input layout

示例1：预期的输入文件结构

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

Troubleshooting

故障排除

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。