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Nextflow demos

This repository demonstrates a few simple Nextflow pipelines for large data image processing, mainly for working with the n5/zarr image formats.

Quick Start

The only software requirements for running this pipeline are Nextflow (version 20.10.0 or greater) and Singularity (version 3.5 or greater). If you are running in an HPC cluster, ask your system administrator to install Singularity on all the cluster nodes.

To install Nextflow:

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

Alternatively, you can install it as a conda package:

conda create --name nf-demos -c bioconda nextflow

To install Singularity on CentOS Linux:

sudo yum install singularity

Clone the multifish repository with the following command:

git clone https://github.com/JaneliaSciComp/nf-demos.git

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

./setup.sh

You can now launch a pipeline, e.g.:

./n5-tools-dask/tiff-to-n5.nf.nf [arguments]