Overview
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R session information
1
Quick Start
1.1
Setup
1.2
Configuration
1.3
Default Parameters
2
Setup Details
2.1
Requirements
2.1.1
Local run
3
All Command Options
3.1
Mandatory Parameters
3.2
Nextflow Options
4
Pipeline Overview
4.1
Main Workflow Steps
5
Annotation
6
Inputs
7
Pipeline Outputs
8
Configuration
8.1
Specifying Options for your Cluster
8.1.1
Time
8.1.2
Cluster-specific options
9
Software
9.1
Software Versions
9.1.1
Prerequisites
9.1.2
Modifying
main.nf
10
Help
10.1
Common Errors
10.2
Resuming
10.2.1
Trouble resuming?
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7
Pipeline Outputs
A bgzipped vcf file for every chromosome with the variants that passed qc.
An index corresponding to every vcf file.
An updated samples sheet.