Janis
translate-docs
  • Welcome to Janis!
  • About
  • Quickstart Guide
  • Pipeline concepts

Tutorials: Translation

  • CWL to Nextflow
    • Tool - Samtools Flagstat
    • Tool - GATK HaplotypeCaller
    • Workflow - Align Sort Markdup
  • 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
  • Docs »
  • Translating CWL to Nextflow
  • Edit on GitHub

Translating CWL to NextflowΒΆ

CWL to Nextflow

  • Tool - Samtools Flagstat
    • Sections
    • Introduction
    • Running Janis Translate
    • Manual Adjustments to Translated Tool
    • Running Translated Tool as a Workflow
    • Conclusion
  • Tool - GATK HaplotypeCaller
    • Sections
    • Introduction
    • Running Janis Translate
    • Manual Adjustments to Translated Tool
    • Running Translated Tool as a Workflow
    • Conclusion
  • Workflow - Align Sort Markdup
    • Sections
    • Introduction
    • Running Janis Translate
    • Translation Output
    • Running the Translated Workflow
    • Manual Adjustments
    • Error 1: Process Order
    • Error 2: Unquoted Strings
    • Error 3: Filename Clashes
    • Completed Workflow
    • Conclusion
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