Nextflow pipeline wrapper for saalfeldlab/n5-spark. Currently it only supports converting a TIFF series into an N5.
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 nextflow -c bioconda nextflow
To install Singularity on CentOS Linux:
sudo yum install singularity
Now you can run the pipeline and it will download everything else it needs:
nextflow run JaneliaSciComp/nf-n5-spark --indir /path/to/tiffs --outdir ./output -profile singularity