https://github.com/janeliascicomp/nf-demos
Nextflow Demo Pipelines for Image Processing
https://github.com/janeliascicomp/nf-demos
image-processing nextflow
Last synced: 5 months ago
JSON representation
Nextflow Demo Pipelines for Image Processing
- Host: GitHub
- URL: https://github.com/janeliascicomp/nf-demos
- Owner: JaneliaSciComp
- Created: 2021-04-06T21:31:07.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2023-12-21T22:46:14.000Z (over 2 years ago)
- Last Synced: 2025-06-02T07:20:03.556Z (about 1 year ago)
- Topics: image-processing, nextflow
- Language: Nextflow
- Homepage:
- Size: 96.7 KB
- Stars: 2
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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](https://www.nextflow.io) (version 20.10.0 or greater) and [Singularity](https://sylabs.io) (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](https://www.nextflow.io/docs/latest/getstarted.html):
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](https://sylabs.io/guides/3.7/admin-guide/installation.html) 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]