A portable, scalable eukaryotic genome annotation pipeline implemented in Nextflow.
This repository contains a fork of companion, a pipeline for automatic eukaryotic parasite annotation by the Sanger Institute.
See companion.sanger.ac.uk for documentation and more information.
The purpose of this fork is to study numerical stability and replicability of bioinformatics pipelines across different executions platforms.
The pipeline is built on Nextflow as a workflow engine, so it needs to be installed first:
export NXF_VER=0.22.0
curl -fsSL get.nextflow.io | bash
With Nextflow installed, the easiest way to use the pipeline is to use the prepared Docker container (https://hub.docker.com/r/satta/companion/) which contains all external dependencies.
docker pull sangerpathogens/companion@sha256:0d79b408bc2349c57854582769c2083619a246c0f857d76f928238e6e2640287
The pipeline has been tested in different Unix-like operating systems with and without Docker containers.
The pipeline can be launched in any system that has the Docker engine installed with this command:
$ nextflow run cbcrg/companion -revision nbt-docker
The pipeline was executed in Amazon Linux (version 2016.03) by using the following command:
$ nextflow run cbrg/companion -revision nbt-awslinux
In the Linux image were installed the Companion dependencies listed in here. The Amazon AMI
is publically available in the EU (Dublin) AWS region with the ID ami-1c364e6f.
The pipeline was executed in a Mac OSX by using the following command:
$ nextflow run cbcrg/companion -revision nbt-macosx
In the computer were installed the Companion dependencies listed in here.