Janis

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Welcome to Janis!
About
Quickstart Guide
Pipeline concepts

Tutorials: Translation

CWL to Nextflow
Galaxy to Nextflow

Tutorials: API

Introduction to Janis
Building a Workflow
Wrapping a new tool
Naming and organising outputs
Adding a tool to a toolbox
Running your workflow
Containerising a tool

Shed / Toolbox

Pipelines
Tools
Data Types
Templates
List of operators
Janis Shed and Toolboxes

API documentation

Framework Documentation
Workflow
Command Tool
Python Tool
Janis Prepare
Expressions
Scattering
Secondary / Accessory Files
Unit Test Framework

Guides

Configuring Janis Assistant
Configuring resources (CPU / Memory)
Call Caching
Common Workflow Language
Workflow Description Language
Engine support
Updating Janis
Frequently asked questions
Common errors
Parsing CWL

Development

Development
Contributing
Testing
Releasing Janis

Janis

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