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TAFFISH is an open bioinformatics tool and workflow ecosystem for building, sharing, and running reproducible analyses with versioned apps, containerized runtime environments, and a lightweight shell-native workflow language.

It sits between ad-hoc shell scripts and heavyweight workflow systems: close enough to the command line for everyday bioinformatics work, but structured enough to make tools, environments, parameters, and workflows reusable.

• Start Here
• What TAFFISH Provides
• Installation
• How TAFFISH Hub Works
• For Users
• For App Developers
• Paper
• Project Status

• A small workflow language for composing bioinformatics tools and flows.
• taf, a local package manager and runner for TAFFISH apps.
• Versioned app releases using the version-release form, such as 0.1.0-r1.
• Container-aware execution through Apptainer, Podman, or Docker backends.
• Hub indexing so users can discover, update, install, and inspect apps from a static GitHub-hosted index.
• Flow dependency metadata so taf install can resolve required app versions automatically.
• Runtime mirror configuration for China/Gitee or internal Git service mirrors.

Install the TAFFISH CLI from taffish/taffish. That repository is the canonical place for current installers, supported platforms, runtime dependencies, container backend notes, and troubleshooting.

Quick user install:

curl -fsSL https://raw.githubusercontent.com/taffish/taffish/main/install/install-taffish.sh | sh -s -- --user

System install for shared servers:

curl -fsSL https://raw.githubusercontent.com/taffish/taffish/main/install/install-taffish.sh | sudo sh -s -- --system

Pinned 0.2.1 install:

curl -fsSL https://raw.githubusercontent.com/taffish/taffish/main/install/install-taffish.sh | sh -s -- --version 0.2.1 --user

For users in China, the Gitee installer downloads from the Gitee mirror and can initialize the China mirror profile:

curl -fsSL https://gitee.com/taffish-org/taffish/raw/main/install/install-taffish.gitee.sh | sh -s -- --user

China/Gitee system install:

curl -fsSL https://gitee.com/taffish-org/taffish/raw/main/install/install-taffish.gitee.sh | sudo sh -s -- --system

macOS note: Gitee may require login for anonymous raw downloads of large binary files. If the Gitee installer fails on macOS with a 403 error or a large-file login message, use the GitHub installer with a working network/proxy, or log in to Gitee and download the macOS binary manually. The Gitee installer is currently most useful for Linux amd64 servers, whose binaries are much smaller and are usually unaffected.

After taf is available locally, the usual starting point is:

taf doctor
taf update
taf search <keyword>
taf install <app>
taf info <app>
taf list

TAFFISH 0.2.1 also supports persistent mirror configuration:

taf config init --china --force
taf update

The runtime config can change the index URL used by taf update and rewrite canonical GitHub app repository URLs during taf install, which makes Gitee or internal Git service mirrors possible without changing the official index schema.

For a guided first run, read the TAFFISH Quick Start.

TAFFISH Hub is currently GitHub-based.

1. Each app lives in its own repository with a root taffish.toml.
2. App repositories publish release tags such as v0.1.0-r1.
3. App repositories build container images in their own GitHub Actions workflows.
4. taffish-index scans the organization and writes static JSON index files.
5. Users run taf update, then install and run apps locally through taf.

The public web Hub at taffish.github.io is the human-facing browser for this ecosystem. The index repository is the machine-facing data source.

Use TAFFISH Hub to browse available apps and use taf locally to install and run them. For installation, CLI behavior, .taf syntax, container usage, and troubleshooting, read taffish/taffish-docs.

TAFFISH app projects are structured repositories with taffish.toml, src/main.taf, docs/help.md, target/ build artifacts, versioned release tags, and optional metadata for dependencies, platform constraints, containers, and upstream software sources.

The official Hub is curated by the taffish organization. At the moment, publishing to the official Hub is limited to organization members. Developers who want to contribute apps can contact the maintainer to discuss joining the organization or publishing strategy.

The TAFFISH project is described in the bioRxiv preprint:

TAFFISH: A lightweight, modular, and containerized workflow framework for reproducible bioinformatics analyses

Authors: Kaiyuan Han, Ting Wang, Shi-Shi Yuan, Cai-Yi Ma, Wei Su, Kejun Deng, Xiaolong Li, Hao Lv, and Hao Lin.

TAFFISH is under active development. The current public infrastructure is built around GitHub repositories, GitHub Actions, GitHub Packages, GitHub Pages, and a static package index. A dedicated server-backed Hub may become useful later, but the current design intentionally keeps the publishing and indexing path simple, auditable, and easy to reproduce.