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
  • Docs »
  • common
  • Edit on GitHub

commonΒΆ

Automatically generated index page for common:

Align and sort reads BwaAligner

(1 versions) v1.0.0


Bwa mem + Samtools View BwaMemSamtoolsView

(1 versions) v0.7.17|1.9


Concat Strelka Somatic Vcf ConcatStrelkaSomaticVcf

(1 versions) v0.1.16


Filter Vardict Somatic Vcf FilterVardictSomaticVcf

(1 versions) v1.9


GATK Base Recalibration on Bam GATKBaseRecalBQSRWorkflow

(2 versions) v4.1.3


Index Fasta reference IndexFasta

(1 versions) v1.0.0


Merge and Mark Duplicates mergeAndMarkBams

(3 versions) v4.1.3



Revision bdefef3a.

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