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TAFFISH brings reproducibility back to shell-based bioinformatics commands.

TAFFISH stands for Tools And Flows Framework Intensify SHell. It is a shell-native reproducible execution and delivery layer for bioinformatics command-line tools and lightweight workflows.

TAFFISH does not try to replace shell scripting or existing workflow systems. Instead, it turns tool calls, parameters, container runtimes, metadata, and versioned releases into installable, distributable, composable, and verifiable executable packages that still behave like ordinary shell commands.

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

The TAFFISH Flow Portal is the human-facing entry point for official flow families. It maps problem-oriented routes built from installable TAFFISH command packages, while the underlying execution still comes from ordinary taf-* commands and explicit input/output contracts.

The portal links:

• official route families such as RNA-seq, NGS QC, BAM QC, BLAST, and phylogeny;
• flow-specific pages and example reports when a route has a mature public case;
• the deeper RNA-seq Flow Family site, which remains the most complete public flow-family case study.

• Command-level reproducibility for the shell commands bioinformaticians already use.
• A .taf language and taffish compiler for packaging command interfaces as shell-native executable apps.
• taf and TAFFISH Hub for discovering, installing, inspecting, and running versioned tools and lightweight flows.
• Container-aware execution through Docker, Podman, or Apptainer, with metadata for versions, dependencies, platforms, smoke checks, and trust signals.
• An open Common Lisp implementation and a conservative taffish-mcp interface for AI-assisted project inspection.

For detailed CLI behavior, .taf syntax, container runtime options, mirrors, MCP setup, security details, source builds, and release-specific changes, use taffish/taffish-docs and the taffish/taffish README.

Install the TAFFISH CLI from taffish/taffish. That repository is the canonical place for source code, current installers, supported platforms, release versions, runtime dependencies, container backend notes, network notes, source-build instructions, release verification, 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

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

China/Gitee note: the Gitee mirror is provided for environments where GitHub raw content is slow or blocked. Some mirror services may restrict anonymous raw downloads of large files, especially for larger macOS binaries. If the Gitee installer cannot fetch a binary, use the GitHub installer with a working network/proxy, download manually after logging in to the mirror, or check the current notes in the taffish/taffish README.

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

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

For pinned releases, platform-specific requirements, China/Gitee notes, mirror configuration, source builds, release verification, container backend behavior, private/local app installs, and troubleshooting, use the current taffish/taffish README and TAFFISH documentation.

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

TAFFISH Hub is currently GitHub-based. It publishes executable package metadata for local taf commands rather than running user jobs on a server.

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, validates new versions, records dependency, platform, container digest, smoke, trust, and upstream metadata, 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 executable packages 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 executable-package repositories with taffish.toml, src/main.taf, docs/help.md, target/ build artifacts, versioned release tags, and optional metadata for dependencies, platform constraints, containers, smoke checks, Hub trust status, 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 open source and under active development. The local CLI/compiler implementation is published in taffish/taffish under Apache License 2.0. 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.