JaneliaSciComp/spots_rsfish
modulePrecise, interactive, fast, and scalable FISH spot detection
spatial transcriptomics spatial genomics FISH Spark
Module Information
Inputs
| Name | Type | Description |
|---|---|---|
| ch_meta | tuple | Channel of tuples containing a meta map and spot detection parameters. Structure: [ val(meta), path(input_image), val(input_dataset), path(spots_output_dir), val(spots_result_name), val(spots_channels), val(spark) ] - meta: map with sample metadata (must include 'id') - input_image: path to the input N5/Zarr image - input_dataset: dataset path within the image container - spots_output_dir: output directory for spot results (staged as 'spots/*') - spots_result_name: name of the output CSV file; defaults to '<meta.id>-points.csv' if empty - spots_channels: comma-separated list of channel indices to include; if empty all channels are used - spark: map with Spark cluster configuration (uri, work_dir, parallelism, executor_cores, executor_memory, driver_cores, driver_memory) |
Outputs
| Name | Type | Description |
|---|---|---|
| params | tuple | Tuple echoing back key parameters for downstream chaining. Structure: [ val(meta), env(INPUT_IMG), val(input_dataset), path(spots_output_dir), val(spots_result_name), val(spark) ] |
| csv | tuple | Tuple of the meta map and the full path to the output CSV file produced by RS-FISH. Structure: [ val(meta), env(full_output_filename) ] |
| versions | file | File containing software versions |
Quick Start
Include this module in your Nextflow pipeline:
include { SPOTS_RSFISH } from 'https://github.com/JaneliaSciComp/nextflow-modules/tree/main/modules/janelia/spots/rsfish'