2.1.1 Overview of vAMPirus execution
vAMPirus is composed of three main components that are recommended to be
deployed sequentially: 1. A startup script to install dependencies and
databases for taxonomy processes, 2. A ‘DataCheck’ pipeline that
provides users with detailed information on data quality and diversity
to inform subsequent analysis, and 3. An ‘Analyze’ pipeline that runs a
comprehensive biology-focused analysis of the data using specified
parameters and program options. vAMPirus is incorporated with Nextflow,
a scientific workflow manager that allows easy configuration and
deployment of the program using Conda, Docker, Singularity or cloud
systems like Amazon Web Services (Di Tommaso et al., 2017). Nextflow
natively communicates with scheduling managers like SLURM, PBS, or
Torque, making it easy to run vAMPirus on high-performance computing
clusters or on a local laptop or workstation. vAMPirus analyses can be
configured using the Nextflow configuration file to promote efficient
utilization of computing resources and reduce run times. Real-time
monitoring and remote launching of vAMPirus analyses can be done using
Nextflow Tower with no alterations to the vAMPirus script.