JaneliaSciComp/spots_fishspots

module

Detects FISH spots in an OME-Zarr image using the easifish spot extraction pipeline

dask FISH spot detection OME-Zarr

Module Information

Repository: https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/spots/fishspots
Source: Janelia
Organization: JaneliaSciComp
Authors: @cgoina , @fleishmang
Maintainers: @cgoina

Spot extraction tools for the EASI-FISH (Expansion-Assisted Iterative fluorescence in situ hybridization) pipeline.

Name	Type	Description
meta	map	Groovy map containing sample metadata. Must include an 'id' field.
input_path	directory	Path to the OME-Zarr image container
input_dataset	string	Dataset subpath within the image container
spots_output_dir	directory	Path to the directory where spot detection results will be written
spots_result_name	string	Name of the output CSV file containing detected spot coordinates. If not specified, defaults to '<meta.id>-points.csv'.
spots_channels	string	Comma separated list of channels to be used for spot extraction. If empty all channels will be included.
spots_image_subpath_ref	string	Reference dataset subpath used for creating the output spots image
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 ([]).
fishspots_config	file	Optional YAML configuration file for the fishspots spot extraction parameters (thresholds, scales, etc.). If not specified, defaults are used.
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.
INPUT_IMG	string	Resolved full path to the input image container
input_dataset	string	Dataset subpath within the image container
spots_output_dir	directory	Path to the directory containing spot detection results
spots_result_name	string	Name of the output CSV file
dask_scheduler	string	Dask scheduler IP address (passed through for downstream processes)
full_output_filename	string	Resolved full path to the output CSV file containing detected spot coordinates
versions	file	File containing software versions

Include this module in your Nextflow pipeline:

include { SPOTS_FISHSPOTS } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/spots/fishspots'