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