software

This module downloads the required tools.

software.checkTools()

Checks if all the needed tools are available.

software.downloadTools()

Downloads and configures all the tools needed by the pipeline.

It downloads the following tools:

  • Java 13

  • FastQC

  • Trimmomatic

  • Hisat2

  • Magic-BLAST

  • Minimap2

  • Qualimap

  • REDItools2

  • JACUSA 2

  • SnpEff