Quickstart

Robbie now uses Nextflow to manage the workflow and can be run on a local system or a supercomputing cluster. You can use a container via singularity, docker, or the host’s software. The current development cycle tests Robbie using singularity on an HPC with the Slurm executor - other setups should work but haven’t been extensively tested.

images.txt

Before running Robbie, you will need to create a text file that contains the paths to each image to be processed. By default, this text file is called images.txt and is in your current directory. You can also give Robbie a custom file name and location using --image_file <path>/<file_name>.txt. For example, if there is a directory named “images” containing the .fits files:

ls images/* > images.txt

will populate images.txt with the image paths relative to the parent directory.

robbie.nf

This file describes the workflow and can be inspected but shouldn’t be edited directly. For an explanation of the command line arguments, run

robbie.nf --help

nextflow.config

This file is the configuration setup and contains all the command line arguments’ default values. You can change these defaults by copying the nextflow.config and editing the relevant params. You can then use your custom config via:

nextflow -C my.config run robbie.nf

The -C my.config directs Nextflow to use only the configuration described in my.config. If you use -c, you can supply a config file that is supplementary to nextflow.config, for example my.config. If both config files have the same parameters defined, my.config takes precedence otherwise the parameters are merged.

-profile

If you’re running Robbie on your local machine, you should use the -profile local option to use the Robbie docker image. For example:

nextflow -C my.config run robbie.nf -profile local

If you’re running Robbie on a supercomputing cluster (HPC), you should use the relevant cluster profile (-profile zeus or -profile magnus) to assure you’re using the cluster’s job queue (such as Slurm). If there isn’t a profile for your cluster (check in nextflow.config), you may have to make your own.