Nextflow wrapper for gatk process.

Pre-requisites

• Nextflow
• Docker

NOTE If you plan to setup a basic server, then you can refer minimal-nextflow-setup

Usage

nextflow run https://github.com/nextflow-hub/gatk

Options

• filePattern

By default, the process assumes the files to follow the *_{R1,R2}.fastq.gz pattern, which could be customized using this option

nextflow run https://github.com/nextflow-hub/gatk --filePattern './*_{1,2}.fastq.gz'

• resultsDir

By default, it stores the result files locally inside the results directory.

nextflow run https://github.com/nextflow-hub/gatk --resultsDir /path/to/custom/resultsDir

• saveMode

By default, the pipeline publishes the results in the resultsDir by copying the relevant output.

You can update this behavior by simply specifying the alternative such as move or link etc.

nextflow run https://github.com/nextflow-hub/gatk --saveMode move

For more information please refer Nextflow documentation

Customizing the script

The sole purpose of process wrappers in nextflow-hub is to keep the code small, clean and hackable with some basic knowledge of nextflow scripting.

If you have specific requirements, you are encouraged to fork/clone and update your version to accomodate your needs.

Contribution

Contribution, in all forms, is most welcome!