Audience
Professionals in science and bioinformatics seeking a computation pipeline library solution
About ruffus
Ruffus is a computation pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics. Ruffus is designed to allow scientific and other analyses to be automated with the minimum of fuss and the least effort. Suitable for the simplest of tasks. Handles even fiendishly complicated pipelines which would cause make or scons to go cross-eyed and recursive. No "clever magic", no pre-processing. Unambitious, the lightweight syntax which tries to do this one small thing well. Ruffus is available under the permissive MIT free software license. This permits free use and inclusion even within proprietary software. It is good practice to run your pipeline in a temporary, “working” directory away from your original data. Ruffus is a lightweight python module for building computational pipelines. Ruffus requires Python 2.6 or higher or Python 3.0 or higher.
Other Popular Alternatives & Related Software
Mako
It provides a familiar, non-XML syntax that compiles into Python modules for maximum performance. Mako's syntax and API borrows from the best ideas of many others, including Django and Jinja2 templates, Cheetah, Myghty, and Genshi. Conceptually, Mako is an embedded Python (i.e. Python Server Page) language, which refines the familiar ideas of componentized layout and inheritance to produce one of the most straightforward and flexible models available, while also maintaining close ties to Python calling and scoping semantics. As templates are ultimately compiled into Python bytecode, Mako's approach is extremely efficient and was originally written to be just as fast as Cheetah. Today, Mako is very close in speed to Jinja2, which uses a similar approach and for which Mako was an inspiration. Can access variables from their enclosing scope as well as the template's request context
Learn more about Mako
Illumina Connected Analytics
Store, archive, manage, and collaborate on multi-omic datasets. Illumina Connected Analytics is a secure genomic data platform to operationalize informatics and drive scientific insights. Easily import, build, and edit workflows with tools like CWL and Nextflow. Leverage DRAGEN bioinformatics pipelines. Organize data in a secure workspace and share it globally in a compliant manner. Keep your data in your cloud environment while using our platform. Visualize and interpret your data with a flexible analysis environment, including JupyterLab Notebooks. Aggregate, query, and analyze sample and population data in a scalable data warehouse. Scale analysis operations by building, validating, automating, and deploying informatics pipelines. Reduce the time required to analyze genomic data, when swift results can be a critical factor. Enable comprehensive profiling to identify novel drug targets and drug response biomarkers. Flow data seamlessly from Illumina sequencing systems.
Learn more about Illumina Connected Analytics
Seqera
Seqera is a bioinformatics platform developed by the creators of Nextflow, designed to streamline and enhance the management of scientific data analysis workflows. It offers a comprehensive suite of tools, including the Seqera Platform for orchestrating scalable data pipelines, Seqera Pipelines for accessing a curated collection of open source workflows, Seqera Containers for simplifying container management, and Seqera Studios for interactive data analysis environments. It supports seamless integration with various cloud and on-premises infrastructures, ensuring reproducibility and compliance in scientific research. Integrate Seqera into existing on-premises systems and cloud platforms like AWS, GCP, and Azure, with no forced migrations. Maintain full control over data residency and scale globally, without compromising security or performance.
Learn more about Seqera
Thoa
Thoa is a cloud bioinformatics platform that solves the six most expensive problems researchers face daily: environment and dependency conflicts, pipeline management, reproducibility, scaling compute, collaboration, and data sharing.
Run Nextflow and Snakemake workflows on managed cloud infrastructure (up to 12TB RAM) with zero DevOps setup. Thoa's AI-assisted debugger resolves environment issues in real time, so pipelines don't crash hours into execution. Every run automatically captures its full execution context: data, software versions, environment, and machine config.
Share complete analyses with collaborators in one click. Recipients can view and re-run results without creating an account or mirroring infrastructure. Supports Docker, Conda, Singularity, Python, and R.
Learn more about Thoa
Pricing
Starting Price:
Free
Free Version:
Free Version available.
Integrations
Company Information
ruffus
www.ruffus.org.uk
Videos and Screen Captures
Other Useful Business Software
Train ML Models With SQL You Already Know
Build and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
Product Details
Platforms Supported
Windows
Mac
Linux
Training
Documentation
Support
Online
ruffus Frequently Asked Questions
Q: What kinds of users and organization types does ruffus work with?
ruffus works with these users and organization types: Mid Size Business, Small Business, Enterprise, Freelance, Nonprofit, Government, and Startup.
Q: What languages does ruffus support in their product?
ruffus supports these languages: English.
Q: What kind of support options does ruffus offer?
ruffus offers support via online.
Q: What other applications or services does ruffus integrate with?
ruffus integrates with: Python.
Q: What type of training does ruffus provide?
ruffus provides training in the form of documentation.
Q: How much does ruffus cost?
Pricing for ruffus starts at Free.
