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bam-qc-flow

A foundation alignment quality-control route for coordinate-sorted BAM files. It checks file integrity, mapping statistics, contig and region summaries, coverage distribution, MultiQC output, a standalone TAFFISH report, and complete provenance. 面向 coordinate-sorted BAM 的基础比对质控路线：检查文件完整性、mapping 统计、contig 与 region 摘要、覆盖度分布、MultiQC、独立 TAFFISH 报告和完整溯源记录。

Full report 完整示例报告 MultiQC report MultiQC 报告 GitHub GitHub

Flow version 流程版本 0.2.0-r1

Example samples 示例样本 1 indexed BAM 1 个带索引 BAM

Region mode 区域模式 enabled in example 示例中已启用

Default route 默认路线 Samtools -> mosdepth -> MultiQC

Route 流程路线

This flow is designed for alignment deliverable checks before variant calling, expression summary, genome coverage review, or downstream interpretation. 这个流程适合在变异检测、表达摘要、基因组覆盖度检查或后续解释之前，对比对交付物做验收。

Input BAM 输入 BAM sorted, indexed BAM files 已排序且带索引 BAM

Integrity 完整性 samtools quickcheck

Alignment stats 比对统计 flagstat / stats / idxstats

Coverage 覆盖度 samtools coverage / mosdepth

Report 报告 TAFFISH report plus MultiQC TAFFISH 报告 + MultiQC

Inputs 输入

Use a BAM table for multiple samples or direct BAM input for a compact run. Region BED files enable target-level coverage summaries. 多样本建议使用 BAM 表；小规模运行可直接传 BAM。提供 BED 后可以生成靶区级覆盖度摘要。

Outputs 输出

Samtools quickcheck, flagstat, stats, idxstats, coverage tables, mosdepth genome and region summaries, MultiQC, logs, commands, versions, methods, and a standalone HTML report. 输出 quickcheck、flagstat、stats、idxstats、coverage 表、mosdepth genome/region 摘要、MultiQC、日志、命令、版本、方法记录和独立 HTML 报告。

Scientific boundary 科学边界

BAM QC identifies technical alignment and coverage signals. It does not by itself decide variant, expression, or biological interpretation quality. BAM 质控识别比对和覆盖度层面的技术信号，本身不直接判断变异、表达或生物学解释质量。

Parameter Guide 参数说明

Stable top-level options define input, outdir, threads, and optional regions; advanced @step: blocks pass extra native arguments into specific tool call sites. 稳定顶层参数定义输入、输出目录、线程和可选 region；高级 @step: 参数块用于把额外原生命令参数传给具体工具调用点。

--samples PATH
--bam PATH

Use a table for multi-sample runs; use direct BAM input for a one-off check. 多样本运行使用样本表；单次检查可直接传 BAM。

Inputs are recorded under 00_inputs/ and all generated files stay inside outdir. 输入记录写入 00_inputs/，所有新产物都留在输出目录中。

--outdir PATH
--force

Choose one output directory for the run. 为一次运行选择一个输出目录。

Existing output directories are refused unless --force is set. 已有输出目录默认拒绝；确认覆盖时才使用 --force。

--regions PATH
--threads N

Add target regions for mosdepth region summaries and set shared thread budget. 添加靶区 BED 以生成 mosdepth region 摘要，并设置共享线程数。

Genome-level summaries are still generated when region mode is used. 启用 region 模式时仍会保留 genome-level 摘要。

@samtools-flagstat-step:
@samtools-stats-step:
@samtools-coverage-step:

Pass advanced native options into selected Samtools call sites. 向指定 Samtools 调用点传递高级原生命令参数。

These blocks are empty by default and should not replace flow-managed inputs or outputs. 这些参数块默认为空，不应用来覆盖流程管理的输入输出参数。

@mosdepth-genome-step:
@mosdepth-regions-step:
@multiqc-step:

Customize mosdepth and MultiQC behavior when a project needs extra native options. 项目需要额外原生命令参数时，可微调 mosdepth 和 MultiQC 行为。

Use sparingly; defaults are intended to be reproducible and easy to audit. 谨慎使用；默认路线以可复现和易审计为目标设计。

Real Example Report 真实示例报告

This report is copied from the flow's real local example output. It shows the TAFFISH-level summary, native MultiQC evidence, deliverables, methods, and provenance together. 这个报告来自流程真实本地示例输出，把 TAFFISH 层摘要、原生 MultiQC 证据、交付物、方法和溯源记录放在一起。

Run Locally 本地运行

Install from the Hub index, inspect help, then run with explicit inputs and outdir. 从 Hub 索引安装，先阅读 help，再用显式输入和输出目录运行。

taf update
taf install bam-qc-flow
taf-bam-qc-flow --help

taf-bam-qc-flow \
  --samples bams.tsv \
  --regions targets.bed \
  --outdir bam-qc-out \
  --threads 4

bam-qc-flow checks alignment deliverables and coverage patterns. Use it as a technical gate before stronger biological claims or downstream analysis. bam-qc-flow 用于检查比对交付物和覆盖度模式。它适合作为更强生物学结论或下游分析前的技术关卡。