TAFFISH flow page TAFFISH 流程主页

ngs-qc-flow

A foundation FASTQ quality-control route for single-end and paired-end sequencing data. It combines raw read statistics, FastQC, optional fastp cleaning, clean-read checks, MultiQC, a standalone TAFFISH report, and complete provenance. 面向单端和双端测序数据的基础 FASTQ 质控路线：原始 reads 统计、FastQC、可选 fastp 清洗、清洗后检查、 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 2 samples, 3 FASTQ files 2 个样本，3 个 FASTQ 文件

Embedded reports 嵌入报告 9 native HTML reports 9 个原生 HTML 报告

Default route 默认路线 SeqKit -> FastQC -> fastp -> MultiQC

Route 流程路线

This flow is designed as a first-pass read inspection layer before RNA-seq, WGS, metagenomics, or a custom downstream route. 这个流程适合作为 RNA-seq、WGS、宏基因组或自定义下游路线之前的第一层 reads 检查。

Input FASTQ 输入 FASTQ single-end, paired-end, tables 单端、双端或样本表

Raw QC 原始质控 SeqKit / FastQC

Cleaning 清洗 fastp optional

Aggregation 汇总 MultiQC

Report 报告 TAFFISH shell plus native reports TAFFISH 外壳 + 原生报告

Inputs 输入

Use direct FASTQ parameters for small runs, or a sample table for multi-sample single-end and paired-end QC. 小规模运行可以直接传 FASTQ；多样本单端/双端质控建议使用样本表。

Outputs 输出

Raw and cleaned statistics, optional cleaned FASTQ files, FastQC and fastp outputs, MultiQC, logs, commands, versions, methods, and a standalone HTML report. 输出原始和清洗后统计、可选清洗后 FASTQ、FastQC/fastp 结果、MultiQC、日志、命令、版本、方法记录和独立 HTML 报告。

Scientific boundary 科学边界

QC flags potential read-level issues. It does not decide whether a project is biologically valid or replace downstream domain-specific interpretation. 质控只能提示 reads 层面的潜在问题，不能直接判断项目生物学结论是否成立，也不能替代下游领域解释。

Parameter Guide 参数说明

Stable top-level options define the flow contract; advanced @step: blocks pass extra native arguments into specific tool call sites. 稳定顶层参数定义流程契约；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
--fastq PATH

Use a table for multi-sample runs; use direct FASTQ inputs for compact one-off checks. 多样本运行使用样本表；临时小规模检查可直接传 FASTQ。

The flow normalizes input files under 00_inputs/. 流程会把输入记录规范化到 00_inputs/。

--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。

--clean true|false
--threads N

Enable fastp cleaning and set the shared thread budget for supported steps. 启用 fastp 清洗，并为支持多线程的步骤设置线程数。

Cleaned FASTQ outputs and clean-read QC are produced only when cleaning is enabled. 只有启用清洗时才会生成清洗后 FASTQ 和清洗后质控结果。

@raw-fastqc-step:
@fastp-pe-step:
@fastp-se-step:

Pass advanced native options into raw FastQC or fastp call sites. 向原始 FastQC 或 fastp 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。

@clean-fastqc-step:
@multiqc-step:

Customize clean-read FastQC or final MultiQC behavior when necessary. 必要时微调清洗后 FastQC 或最终 MultiQC 行为。

Use sparingly; the default route is meant to be reproducible and inspectable. 谨慎使用；默认路线已经以可复现和可检查为目标设计。

Real Example Report 真实示例报告

This report is copied from the flow's real local example output. It shows how TAFFISH wraps native QC reports inside one standalone reading surface. 这个报告来自流程真实本地示例输出，展示 TAFFISH 如何把原生质控报告收束到一个可独立阅读的页面中。

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 ngs-qc-flow
taf-ngs-qc-flow --help

taf-ngs-qc-flow \
  --samples samples.tsv \
  --outdir ngs-qc-out \
  --clean true \
  --threads 4

ngs-qc-flow is a QC and reporting route, not a downstream interpretation engine. Use it to decide whether reads are technically ready for a next analysis layer. ngs-qc-flow 是质控和报告路线，不是下游生物学解释引擎。它用于判断 reads 是否在技术层面适合进入下一层分析。