Description

The module compiles segmentation tiles 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

algorithm_json{:bash}

:file

JSON file containing the algorithm parameters.

*.json

segmentation_tiles{:bash}

:file

Parquet files containing the segmentation results for tiles to compile.

*.parquet

Output

name:type
description
pattern

mosaic_space{:bash}

meta{:bash}

:map

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

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

:file

Parquet file containing the compiled segmentation results in mosaic space.

micron_space{:bash}

meta{:bash}

:map

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

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

:file

Parquet file containing the compiled segmentation results in micron space.

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user mcmero
get in touch
Ask a question on Slack Open an issue on GitHub