How to run the pipeline

The autodatabase pipeline requires Nextflow and either Docker or Singularity.

Installing Nextflow, Docker and Singularity

Nextflow can run on Mac OSX and Linux-based systems. It requires at java>=8 (java -version to check). To install Nextflow:

curl -s https://get.nextflow.io | bash

This creates an executable nextflow file, you can then move the nextflow file to a directory accessible by your $PATH variable.

The autodatabase pipeline uses Nextflow DSL2 and requires Nextflow>=20.01.0. To check your version of Nextflow run nextflow -version. To update Nextflow run nextflow -self-update

To installation instructions for Docker can be found here. Singularity requires Go to compile; the installation instructions for Singularity can be found here.

Setting the parameters

There are three global parameters needed to run autodatabase which are set in nextflow.config:

• params.addFasta The directory containing the assemblies to be added to the database. Should consist of sub-directories where the fastas are sorted into named directories for each taxon
• params.newDatabase The directory where the results of the workflow will be saved. The default is ${baseDir}/results.
• params.previousDatabase Autodatabase can build on top of the fasta files from a previous database build. If there is no previous database build then set to null

Running the pipeline

To run the pipeline:

nextflow run main.nf -profile [docker, singularity]

The parameters can also be set on the command line like so

nextflow run main.nf -profile [docker, singularity] --addFasta path/to/fasta --previousDatabase path/to/previous/database --newDatabase path/for/output

overriding nextflow.config