JaneliaSciComp/omezarrtools_multiscale

module

Generates a multiscale pyramid for an OME-Zarr container

dask image formats OME-Zarr multiscale pyramid

Module Information

Repository: https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/omezarrtools/multiscale
Source: Janelia
Organization: JaneliaSciComp
Authors: @cgoina
Maintainers: @cgoina

Tools for working with Zarr and OME-Zarr arrays.

Name	Type	Description
meta	map	Groovy map containing sample metadata. Must include an 'id' field.
data_container	directory	Path to the OME-Zarr container for which to generate the multiscale pyramid
dataset_subpath	string	Relative path to the dataset within the container (for N5 or Zarr containers). Pass as empty string if the dataset is at the root of the container.
dask_scheduler	string	Dask scheduler IP address. If not using a distributed cluster, pass as empty string.
dask_config	file	Optional path to a dask configuration file. If not specified, pass as empty list ([]).
cpus	integer	Number of CPUs to allocate for the process
mem_gb	integer	Amount of memory in GB to allocate for the process

Name	Type	Description
meta	map	Groovy map containing sample metadata. Must include an 'id' field.
full_data_container_path	string	Resolved full path to the OME-Zarr container
dataset_subpath	string	Relative path to the dataset within the container
versions	file	File containing software versions

Include this module in your Nextflow pipeline:

include { OMEZARRTOOLS_MULTISCALE } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/omezarrtools/multiscale'