Description

The module runs the segmentation algorithm on a specific tile using Vizgen’s post-processing tool.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘sample1’, single_end:false ]

input_images{:bash}

:directory

Path to the input images directory to be used for segmentation.

segmentation_params{:bash}

:file

Path to the segmentation parameters (algorithm specification) JSON file generated by the preparesegmentation module.

*.json

tile_index{:bash}

:integer

The index of the tile to run the segmentation algorithm on.

algorithm_json{:bash}

:file

JSON file containing the algorithm parameters.

*.json

custom_weights{:bash}

:directory

Directory containing custom weights for the segmentation algorithm. Must be defined in the algorithm JSON file under “custom_weights” as directory name only (not full path).

Output

name:type
description
pattern

segmented_tile{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/result_tiles/*.parquet{:bash}

:file

Parquet file containing the segmentation results for the specified tile.

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user mcmero
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