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Quick Start

Nextflow Tower Quick Start

The easiest way to use the EASI-FISH pipeline is by running it from the Nextflow Tower web GUI interface. See the step-by-step instructions here.

Command-line Quick Start

For tech-savvy users, the pipeline can be invoked from the command-line and runs on any workstation or cluster. The only prerequisites for running this pipeline are Nextflow (version 20.10.0 or greater) and Singularity (version 3.5 or greater).

To install Nextflow:

curl -s | bash

Alternatively, you can install it as a conda package:

conda create --name multifish -c bioconda nextflow

To install Singularity on CentOS Linux:

sudo yum install singularity

Once the prerequisites are installed, you should clone this repository with the following command:

git clone

Before running the pipeline for the first time, run setup to pull in external dependencies:


You can now launch the pipeline using:

./ [arguments]

Demo Data Sets

To get running quickly, there are example scripts provided which download EASI-FISH example data and run the full pipeline. You can analyze the smallest data set like this:

./examples/ <data dir> [arguments]

The data dir is the path to where you want to store the data and analysis results. You can add additional arguments to skip steps previously completed or add monitoring with Nextflow Tower. See below for additional details about the argument usage.

The script will download a demo data set and run the full analysis pipeline. It is tuned for a 40 core machine with 128 GB of RAM and runs for about 30 minutes. If your compute resources are different, you may need to edit the script to change the parameters to suit your environment.

After the pipeline runs, you can expect to find 5.8 GB in the data dir:

1.4G     /opt/demo_tiny/inputs
4.4G     /opt/demo_tiny/outputs
320K    /opt/demo_tiny/spark

There is also a with larger data:

23G     /opt/demo_small/inputs
58G     /opt/demo_small/outputs
525M    /opt/demo_small/spark

And a with that requires 209 GB in total:

65G     /opt/demo_medium/inputs
145G    /opt/demo_medium/outputs
665M    /opt/demo_medium/spark