How to use gkno

General gkno usage

Installation: How to install gkno

Overview: How does gkno work?

Pipeline help: How to find and use available gkno pipelines

gkno arguments: Arguments applicable to all gkno pipelines

Parallel execution: How to run gkno in parallel or on a cluster

Parameter sets

What are they? What are parameter sets and how are they used?

In tool configuration files: How to define parameter sets in tool configuration files?

In pipeline configuration files: How to define parameter sets in pipeline configuration files?

Test parameter sets: Check that gkno pipelines are functioning correctly

Create your own parameter sets: Generate your own parameter sets

Best practice guidelines

Getting started: Find a pipeline starting a run

Tool configuration files

Required attributes: Attributes required in a tool configuration file

Argument attributes: Attributes used to describe tool arguments

Parameter sets: How to define parameter sets in tool configuration files

Create your own: A tutorial on creating a tool configuration file for your own tool

Pipeline configuration files

Describe a pipeline: How to describe a gkno pipeline

Build a pipeline: Step-by-step guide to build the bwa-multi pipeline

Build a pipeline: Guide to including pipelines in your new pipeline

Execution examples

Examples: How to manipulate BAM files

Other help

CSHL BAM tutorial: How to manipulate BAM files

CSHL Practical: Using gkno and iobio to generate and interrogate variant calls

CSHL iobio practical: How to use the iobio tools for data QC and interrogation