Description

The module compiles segmentation tiles using Vizgen’s post-processing tool.

Input

name:type
description
pattern

meta

:map

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

input_images

:directory

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

segmentation_params

:file

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

*.json

algorithm_json

:file

JSON file containing the algorithm parameters.

*.json

segmentation_tiles

:file

Parquet files containing the segmentation results for tiles to compile.

*.parquet

Output

name:type
description
pattern

mosaic_space

meta

:map

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

${prefix}/*_mosaic_space.parquet

:file

Parquet file containing the compiled segmentation results in mosaic space.

micron_space

meta

:map

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

${prefix}/*_micron_space.parquet

:file

Parquet file containing the compiled segmentation results in micron space.

versions

versions.yml

:file

File containing software versions

versions.yml

Tools

maintainer
Github user mcmero
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