nf_ngff_conv

Nextflow NGFF/ome.zarr conversion pipeline

Installation

Prerequisite

Install Nextflow:

(For details see Nextflow - Installation)

Install java:

curl -s https://get.sdkman.io | bash
sdk install java 17.0.10-tem

Get nextflow binary:

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

Additionally:

Install conda:

(For details see Installing Miniconda)

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Install AWS cli

(For details see conda-forge / packages / awscli)

conda install awscli

Clone repository

git clone https://github.com/dominikl/nf_ngff_conv.git
cd nf_ngff_conv

Setup

Setup AWS access (example: EBI Embassy object storage):

aws configure --profile embassy
echo "endpoint_url = https://uk1s3.embassy.ebi.ac.uk" >> ~/.aws/config 

Adjust configuration in nextflow.config.

Run

Run it with:

nextflow run --input idr0157_paths.tsv --column 1 bf2raw.nf

(Where --column 1 means that the second column contains the paths the images. It is assumed that the first column is the dataset name)

Note: idr0157_paths.tsv is an example and only contains the first dataset of idr0157.