Curated flow routes 策划型流程路线

TAFFISH Flow Portal TAFFISH 流程门户

Problem-oriented reference routes composed from reproducible TAFFISH commands. Each flow keeps a stable domain interface while preserving the shell-native, command-level reproducibility that defines TAFFISH. 这里收纳由可复现 TAFFISH 命令组成的问题导向参考路线。每个流程提供稳定领域接口，同时保留 TAFFISH 的原生 shell 命令层级可复现性定位。

This page is a map of official analysis routes, not a new workflow engine layer. The concrete work is still done by normal TAFFISH commands, explicit inputs, and a single output directory. 这个页面是官方分析路线图，不是把 TAFFISH 包装成新的工作流引擎。真正执行仍然来自普通 TAFFISH 命令、显式输入和单一输出目录。

Active families 当前主线

5 available families 5 条可用主线

Default contract 默认约定

one outdir, full provenance 单输出目录 + 完整记录

Audience 面向对象

researchers and maintainers 科研用户与维护者

Official Flow Families 官方流程家族

These routes are meant to be small enough to inspect, serious enough for real examples, and strict about inputs, outputs, logs, versions, and methods. 这些路线希望足够小、足够清楚，也足够真实：输入、输出、日志、版本和方法记录都应能被检查和复现。

RNA-seq Flow Family RNA-seq 流程家族

A modular route from reference/index preparation to quantification, differential expression, enrichment, and report generation. 从参考/index 准备，到定量、差异表达、富集分析和报告生成的模块化路线。

public portal 已有独立页面

Inputs: FASTQ reads, sample sheet, reference genome and annotation. 输入：FASTQ 数据、样本表、参考基因组和注释。
Outputs: QC, indexes, expression matrices, DE tables, enrichment results, report. 输出：质控、索引、表达矩阵、差异分析表、富集结果和报告。
Best use: real RNA-seq case studies and article-facing demonstrations. 适合：真实 RNA-seq 案例、文章展示和用户学习。

Open RNA-seq portal 打开 RNA-seq 页面 Search Hub 搜索 Hub

NGS QC Flow NGS 质控流程

Foundation FASTQ quality-control route for raw read statistics, FastQC, optional fastp cleaning, clean-read checks, MultiQC, and provenance. 基础 FASTQ 质控路线：原始数据统计、FastQC、可选 fastp 清洗、清洗后数据检查、MultiQC 和溯源记录。

available 已可用

Inputs: single-end, paired-end, or multi-sample FASTQ tables. 输入：单端、双端或多样本 FASTQ 表。
Outputs: raw and clean QC metrics, optional cleaned FASTQ, MultiQC report. 输出：原始和清洗后质控指标、可选清洗后 FASTQ、MultiQC 报告。
Best use: first-pass read inspection before RNA-seq, WGS, metagenomics, or custom routes. 适合：RNA-seq、WGS、宏基因组或自定义流程前的 reads 初筛。

Open in Hub 在 Hub 中打开

BAM QC Flow BAM 质控流程

Foundation alignment QC route for coordinate-sorted BAM files using Samtools, mosdepth, MultiQC, fixed output structure, and audit files. 面向已排序 BAM 的基础比对质控路线：Samtools、mosdepth、MultiQC、固定输出结构和审计文件。

available 已可用

Inputs: indexed coordinate-sorted BAM files or a multi-sample BAM table. 输入：带索引的 coordinate-sorted BAM，或多样本 BAM 表。
Outputs: flagstat, stats, idxstats, coverage, optional region summaries, MultiQC. 输出：flagstat、stats、idxstats、coverage、可选区域覆盖摘要、MultiQC。
Best use: alignment deliverable checks before variant calling or downstream interpretation. 适合：变异检测或后续解释前的比对结果验收。

Open in Hub 在 Hub 中打开

BLAST Flow BLAST 流程

Focused local BLAST route that builds a database from FASTA, runs one BLAST+ search command, and writes results plus provenance. 聚焦的本地 BLAST 路线：从 FASTA 构建数据库，运行一次 BLAST+ 搜索，并输出结果与溯源记录。

available 已可用

Inputs: subject FASTA, query FASTA, BLAST program, and optional output format. 输入：数据库 FASTA、查询 FASTA、BLAST 程序和可选输出格式。
Outputs: local BLAST database, tabular hits, commands, versions, and manifest. 输出：本地 BLAST 数据库、命中表、命令、版本和运行记录。
Best use: small reproducible similarity searches and teaching examples. 适合：小型可复现相似性搜索和教学示例。

Open in Hub 在 Hub 中打开

Phylogeny Flow 系统发育流程

A compact evolutionary analysis route for homologous sequences: align, optionally trim, infer a tree, visualize it, and preserve the exact commands. 面向同源序列的紧凑进化分析路线：比对、可选修剪、建树、可视化，并保存完整命令记录。

formal-ready 正式测试路线

Inputs: unaligned or aligned homologous FASTA sequences. 输入：未比对或已比对的同源 FASTA 序列。
Outputs: alignment, trimmed alignment, Newick tree, tree plots, methods and logs. 输出：序列比对、修剪后比对、Newick 树、树图、方法记录和日志。
Best use: teaching, gene-family exploration, and lightweight comparative biology. 适合：教学、基因家族探索和轻量级比较生物学分析。

Open flow page 打开流程主页 Example report 示例报告 Search Hub 搜索 Hub

Candidate Route Map 候选路线图

Future families should be added when the required taf-tools, test data, and output contracts are clear. 后续路线应在 taf-tool、测试数据和输出契约足够明确后再纳入。

planned 计划中

Variant / WGS 变异分析 / WGS

Mapping, BAM processing, variant calling, filtering, annotation, and reports. 比对、BAM 处理、变异检测、过滤、注释和报告。

planned 计划中

Assembly / Annotation 组装 / 注释

Genome assembly checks, annotation preparation, evidence integration, and summaries. 基因组组装检查、注释准备、证据整合和摘要输出。

planned 计划中

Metagenomics 宏基因组

Read QC, taxonomic profiling, abundance tables, diversity summaries, and reports. 质控、物种组成、丰度表、多样性摘要和报告。

planned 计划中

Single-cell RNA-seq 单细胞 RNA-seq

Matrix generation, QC, clustering, annotation handoff, and reproducible reports. 矩阵生成、质控、聚类、注释交接和可复现报告。

planned 计划中

Protein / Structure 蛋白 / 结构

Sequence search, alignment, structural inspection, lightweight visualization, and notes. 序列搜索、比对、结构检查、轻量可视化和结果说明。

Using A Flow 如何使用流程

Install the flow like any other TAFFISH app, read its command help, and run it with an explicit output directory. Flow outputs should stay under that directory, including commands, versions, logs, methods, results, and reports. 流程和普通 TAFFISH 应用一样安装；先阅读命令帮助，再用显式输出目录运行。所有新产物都应留在输出目录内，包括命令、版本、日志、方法记录、结果和报告。

taf update
taf install phylogeny-flow
taf-phylogeny-flow --help

taf install rnaseq-standard-flow
taf-rnaseq-standard-flow --help