modulexcite/awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Awesome Pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

Pipeline frameworks & libraries

• ActionChain - A workflow system for simple linear success/failure workflows.
• Airflow - Python-based workflow system created by AirBnb.
• Anduril - Component-based workflow framework for scientific data analysis.
• Antha - High-level language for biology.
• Bds - Scripting language for data pipelines.
• Bpipe - Tool for running and managing bioinformatics pipelines.
• Briefly - Python Meta-programming Library for Job Flow Control.
• Cluster Flow - Command-line tool which uses common cluster managers to run bioinformatics pipelines.
• Clusterjob - Automated reproducibility, and hassle-free submission of computational jobs to clusters.
• Compss - Programming model for distributed infrastructures.
• Conan2 - Light-weight workflow management application.
• Cosmos - Python library for massively parallel workflows.
• Cromwell - Workflow Management System geared towards scientific workflows from the Broad Institute.
• Cuneiform - Advanced functional workflow language and framework, implemented in Erlang.
• Dockerflow - Workflow runner that uses Dataflow to run a series of tasks in Docker.
• Doit - Task management & automation tool.
• Dagobah - Simple DAG-based job scheduler in Python.
• Drake - Robust DSL akin to Make, implemented in Clojure.
• Flex - Language agnostic framework for building flexible data science pipelines (Python/Shell/Gnuplot).
• Flowr - Robust and efficient workflows using a simple language agnostic approach (R package).
• Gwf - Make-like utility for submitting workflows via qsub.
• Hive - System for creating and running pipelines on a distributed compute resource.
• Joblib - Set of tools to provide lightweight pipelining in Python.
• Ketrew - Embedded DSL in the OCAML language alongside a client-server management application.
• Kronos - Workflow assembler for cancer genome analytics and informatics.
• Loom - Tool for running bioinformatics workflows locally or in the cloud.
• Longbow - Job proxying tool for biomolecular simulations.
• Luigi - Python module that helps you build complex pipelines of batch jobs.
• Makeflow - Workflow engine for executing large complex workflows on clusters.
• Mario - Scala library for defining data pipelines.
• Mistral - Python based workflow engine by the Open Stack project.
• Moa - Lightweight workflows in bioinformatics.
• Nextflow - Flow-based computational toolkit for reproducibile and scalable bioinformatics pipelines.
• NiPype - Workflows and interfaces for neuroimaging packages.
• OpenGE - Accelerated framework for manipulating and interpreting high-throughput sequencing data.
• PipEngine Ruby based launcher for complex biological pipelines.
• Pinball - Python based workflow engine by Pinterest.
• PyFlow - Lightweight parallel task engine.
• PypeFlow - Lightweight workflow engine for data analysis scripting.
• Pwrake - Parallel workflow extension for Rake.
• Qdo - Lightweight high-throughput queuing system for workflows with many small tasks to perform.
• Qsubsec - Simple tokenised template system for SGE.
• Rabix - Python-based workflow toolkit based on the Common Workflow Language and Docker.
• Remake - Make-like declarative workflows in R.
• Rmake - Wrapper for the creation of Makefiles, enabling massive parallelization.
• Rubra - Pipeline system for bioinformatics workflows.
• Ruffus - Computation Pipeline library for Python.
• Ruigi - Pipeline tool for R, inspired by Luigi.
• Sake - Self-documenting build automation tool.
• SciLuigi - Helper library for writing flexible scientific workflows in Luigi.
• Scoop - Scalable Concurrent Operations in Python.
• Snakemake - Tool for running and managing bioinformatics pipelines.
• Spiff - Based on the Workflow Patterns initiative and implemented in Python.
• Stpipe - File processing pipelines as a Python library.
• Suro - Java-based distributed pipeline from Netflix.
• Swift - Fast easy parallel scripting - on multicores, clusters, clouds and supercomputers.
• Toil - Distributed pipeline workflow manager (mostly for genomics).
• Yap - Extensible parallel framework, written in Python using OpenMPI libraries.
• WorldMake - Easy Collaborative Reproducible Computing.

Workflow platforms

• ActivePapers - Computational science made reproducible and publishable.
• Apache Iravata - Framework for executing and managing computational workflows on distributed computing resources.
• Arvados - A container based workflow platform.
• Biokepler - Bioinformatics Scientific Workflow for Distributed Analysis of Large-Scale Biological Data.
• Chipster - Open source platform for data analysis.
• Fireworks - Centralized workflow server for dynamic workflows of high-throughput computations.
• Galaxy - Web-based platform for biomedical research.
• Kepler - Kepler scientific workflow application from University of California.
• NextflowWorkbench - Integrated development environment for Nextflow, Docker and Reusable Workflows.
• OpenMOLE - Workflow Management System for exploration of models and parameter optimization.
• Ophidia - Data-analytics platform with declarative workflows of distributed operations.
• Pegasus - Workflow Management System.
• Sushi - Supporting User for SHell script Integration.
• Yabi - Online research environment for grid, HPC and cloud computing.
• Taverna - Domain independent workflow system.
• VisTrails - Scientific workflow and provenance management system.
• Wings - Semantic workflow system utilizing Pegasus as execution system.

Workflow languages

• Common Workflow Language
• Cloudgene Workflow Language
• OpenMOLE DSL
• Workflow Definition Language
• Yet Another Workflow Language

Workflow standardization initiatives

• Workflow 4 Ever Initiative
• Workflow 4 Ever workflow research object model
• Workflow Patterns Initiative
• Workflow Patterns Library
• ResearchObject.org

Literate programming (aka interactive notebooks)

• Beaker Notebook-style development environment.
• Binder - Turn a GitHub repo into a collection of interactive notebooks powered by Jupyter and Kubernetes
• IPython A rich architecture for interactive computing.
• Jupyter Language-agnostic notebook literate programming environment.
• Pathomx - Interactive data workflows built on Python.
• R Notebooks - R Markdown notebook literate programming environment.
• Wakari - Web-based Python Data Analysis.
• Zeppelin - Web-based notebook that enables interactive data analytics.

Build automation tools

• Bazel - Build software just as engineers do at Google.
• DoIt - Highly generalized task-management and automation in Python.
• Gradle - Unified cross platforms builds.
• Scons - Python library focused on C/C++ builds.
• Shake - Define robust build systems akin to GNU Make using Haskell.
• Make - The GNU Make build system.

Other projects

• HPC Grid Runner
• noWorkflow - Supporting infrastructure to run scientific experiments without a scientific workflow management system, and still get things like provenance.