Welcome to Workflomics’s Documentation

Welcome to the official documentation for Workflomics—a platform designed to empower bioinformaticians in the generation and comparison of computational workflows for life science research.

Introduction

Workflomics addresses the challenges faced by researchers dealing with large and complex datasets by facilitating the creation of optimal data analysis workflows. It integrates bioinformatics tools and metadata with technologies for automated workflow exploration and benchmarking. This innovative approach supports the development of advanced workflows in bioinformatics, particularly within the proteomics domain, enhancing scientific quality, robustness, reproducibility, FAIRness (Findability, Accessibility, Interoperability, and Reusability), and maintainability.

The platform is currently demonstrated on workflomics.org with mass spectrometry-based proteomics as a use case (domain), with metabolomics and mass spectrometry imaging coming soon. However, the Workflomics platform itself is domain-agnostic, aiming to support the wider life sciences community.

Contents

User Guide

• Web Interface
  • Accessing Workflomics
  • How to Use Workflomics
  • Upload Benchmark Results

Workflomics Benchmarker

• How to benchmark workflows
  • Workflomics Benchmarker
  • License
  • Contributors
• Installation guide
  • Prerequisites
  • Installing Python
  • Setting Up a Virtual Environment
  • Installing Workflomics Benchmarker
  • Supporting Containerization
• Use Benchmarker
  • Running Workflows
  • Visualizing Benchmark Results

Domain Expert Guide

• Adding a new tool
  • 1. Find or create a docker image
  • 2. Run the tool inside the container
  • 3. Create the CWL annotation
  • 1. Create a workflow
• Domain Development Guide
  • Overview of Steps
  • Step 1: Clone the Workflomics Repository
  • Step 2: Create a New Domain Folder
  • Step 3: Add Tools to Your Domain
  • Step 4: Configure Domain Files
  • Step 5: Validate the Domain with APE Library
  • Step 6: Submit and Integrate the Domain
  • Configure CWL Files
  • Configure Workflomics

Developer Guide

• Local development and Deployment
  • Development Setup
  • Deployment
• Data Formats and Schemas Overview
  • JSON Schema for Benchmarks
• Pubmetric Documentation
  • Local Setup
  • Graph Generation
  • Metric Calculation
  • File Schemas
• Pubmetric RESTful API
  • Setup
  • Index
  • Score workflows
  • Recreate Graph

Rational

• Annotating Tools
• General Discussions

Note

This project is under active development. Features and documentation are subject to change.

Contributors

The project was developed within the Great Bake Off” of Bioinformatics Workflows project by the project’s core team:

• Vedran Kasalica (v.kasalica[at]esciencecenter.nl),

• Peter Kok,

• Rob Marissen,

• Magnus Palmblad,

• Anna-Lena Lamprecht

and the following contributors: * Nauman Ahmed, * Alma Nilsson, * Felipe Morato