Janis
latest
  • Welcome to Janis!
  • About
  • Pipeline concepts

Tutorials

  • Tutorial 0 - Introduction to Janis
  • Tutorial 1 - Building a Workflow
  • Tutorial 2 - Wrapping a new tool
  • Tutorial 3 - 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
  • Collecting tool outputs
  • Configuring Janis for HPCs
  • Engine support
  • Updating Janis
  • Frequently asked questions
  • Common errors
  • Parsing CWL

Development

  • Development
  • Contributing
  • Testing
  • Releasing Janis
Janis
  • Docs »
  • Illumina
  • Edit on GitHub

IlluminaΒΆ

Automatically generated index page for Illumina:

Bcl2Fastq bcl2fastq

(1 versions) v2.20.0


Hap.py validation happy_validator

(1 versions) v0.3.9


Manta manta

(2 versions) v1.5.0


Manta manta_cram

(2 versions) v1.5.0


Strelka (Germline) strelka_germline

(2 versions) v2.9.10


Strelka (Somatic) strelka_somatic

(2 versions) v2.9.10


Strelka (Somatic) strelka_somatic_cram

(2 versions) v2.9.10



Revision e1ae6b21.

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