Janis
stable
  • 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 »
  • Dawson Labs
  • Edit on GitHub

Dawson LabsΒΆ

Automatically generated index page for Dawson Labs:

Create genomic call regions CreateCallRegions

(1 versions) v0.1.0


Freebayes somatic workflow FreeBayesSomaticWorkflow

(1 versions) v0.1.1


Freebayes somatic workflow (CRAM) FreeBayesSomaticWorkflowCram

(1 versions) v0.1.1


Mutect2 joint somatic variant calling workflow Mutect2JointSomaticWorkflow

(1 versions) v0.1.1


Mutect2 joint somatic variant calling workflow (CRAM) Mutect2JointSomaticWorkflowCram

(1 versions) v0.1.1


Strelka 2Pass analysis Strelka2PassWorkflow

(1 versions) v0.2


Strelka 2Pass analysis (CRAM) Strelka2PassWorkflowCram

(1 versions) v0.2


Call Somatic Variants from freebayes callSomaticFreeBayes

(1 versions) v0.1.8


Refilter Strelka2 Variant Calls refilterStrelka2Calls

(1 versions) v0.1.8



Revision e1ae6b21.

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