nf-core/vizgenpostprocessing_preparesegmentation

module

The module prepares the specification JSON file for Vizgen's post-processing tool cell segmentation workflow.

vpt vizgen segmentation microscopy spatial transcriptomics

Module Information

Repository: https://github.com/nf-core/modules/tree/master/modules/nf-core/vizgenpostprocessing/preparesegmentation
Source: nf-core
Organization: nf-core
Authors: @mcmero
Maintainers: @mcmero

Tools

vizgenpostprocessing

Vizgen's post-processing tool

License: Apache-2.0

Inputs

Name	Type	Description
0
algorithm_json	file	JSON file containing the algorithm specification
images_regex	string	Can either be blank to match files by MERSCOPE convention, or a python formatting string specifying the file name (e.g., image_{stain}_z{z}.tif), or a regular expression matching the tiff files to be used (e.g., mosaic_(?P<stain>[\w\|-]+)_z(?P<z>[0-9]+).tif)

Quick Start

Include this module in your Nextflow pipeline:

include { VIZGENPOSTPROCESSING_PREPARESEGMENTATION } from 'https://github.com/nf-core/modules/tree/master/modules/nf-core/vizgenpostprocessing/preparesegmentation'

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