modules/proseg_proseg

Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.

segmentationspatialtranscriptomics

https://github.com/nf-core/modules/[...]/modules/nf-core/proseg/proseg

Description

Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information

`transcripts`
`:file`

Transcript ids, genes, revised positions, assignment probability, etc.

*transcript-metadata.{csv.gz,csv,parquet}

`mode`
`:string`

Proseg preset mode

`transcript_metadata_fmt`
`:string`

Format of the transcript metadata file

`cell_metadata_fmt`
`:file`

Format of the cell metadata file

`expected_counts_fmt`
`:file`

Format of the expected counts file

Output

name:type

description

pattern

`zarr`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}.zarr`
`:file`

Path to the output spatialdata Zarr file.

*.zarr

`transcript_metadata`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_transcript-metadata.{csv,csv.gz,parquet}`
`:file`

Transcript ids, genes, revised positions, assignment probability, etc.

*transcript-metadata.{csv.gz,csv,parquet}

`cell_polygons`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_cell-polygons.geojson.gz`
`:file`

Path to the cell polygons file.

*cell-polygons.geojson.gz

`cell_metadata`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_cell-metadata.{csv,csv.gz,parquet}`
`:file`

Path to the cell metadata file.

*cell-metadata.{csv.gz,csv,parquet}

`cell_polygons_layers`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_cell-polygons-layers.geojson.gz`
`:file`

Path to the cell polygons layers file.

*cell-polygons-layers.geojson.gz

`expected_counts`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_expected-counts.{csv,csv.gz,parquet}`
`:file`

Path to the expected counts file.

*expected-counts.{csv.gz,csv,parquet}

`union_cell_polygons`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_cell-polygons-union.geojson.gz`
`:file`

Path to the union cell polygons file.

*cell-polygons-union.geojson.gz

`maxpost_counts`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_maxpost-counts.{csv,csv.gz,parquet}`
`:file`

Path to the max posterior counts file.

*maxpost-counts.{csv.gz,csv,parquet}

`output_rates`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_output-rates.{csv,csv.gz,parquet}`
`:file`

Path to the output rates file.

*output-rates.{csv.gz,csv,parquet}

`cell_hulls`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_cell-hulls.{csv,csv.gz,parquet}`
`:file`

Path to the cell hulls file.

*cell-hulls.{csv.gz,csv,parquet}

`gene_metadata`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_gene-metadata.{csv,csv.gz,parquet}`
`:file`

Path to the gene metadata file.

*gene-metadata.{csv.gz,csv,parquet}

`metagene_rates`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_metagene-rates.{csv,csv.gz,parquet}`
`:file`

Path to the metagene rates file.

*metagene-rates.{csv.gz,csv,parquet}

`metagene_loadings`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_metagene-loadings.{csv,csv.gz,parquet}`
`:file`

Path to the metagene loadings file.

*metagene-loadings.{csv.gz,csv,parquet}

`cell_voxels`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_cell-voxels.{csv,csv.gz,parquet}`
`:file`

Path to the cell voxels file.

*cell-voxels.{csv.gz,csv,parquet}

`versions_proseg`

`${task.process}`
`:string`

The name of the process

`proseg`
`:string`

The name of the tool

`proseg --version | sed 's/proseg //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`proseg`
`:string`

The name of the tool

`proseg --version | sed 's/proseg //'`
`:eval`

The expression to obtain the version of the tool

Tools

proseg
GPLv3

Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.

github.com/dcjones/proseg 10.1038/s41592-025-02697-0

modules/proseg_proseg

Description

Input

meta:map

transcripts:file

mode:string

transcript_metadata_fmt:string

cell_metadata_fmt:file

expected_counts_fmt:file

Output

zarr

meta:map

${prefix}.zarr:file

transcript_metadata

meta:map

${prefix}_transcript-metadata.{csv,csv.gz,parquet}:file

cell_polygons

meta:map

${prefix}_cell-polygons.geojson.gz:file

cell_metadata

meta:map

${prefix}_cell-metadata.{csv,csv.gz,parquet}:file

cell_polygons_layers

meta:map

${prefix}_cell-polygons-layers.geojson.gz:file

expected_counts

meta:map

${prefix}_expected-counts.{csv,csv.gz,parquet}:file

union_cell_polygons

meta:map

${prefix}_cell-polygons-union.geojson.gz:file

maxpost_counts

meta:map

${prefix}_maxpost-counts.{csv,csv.gz,parquet}:file

output_rates

meta:map

${prefix}_output-rates.{csv,csv.gz,parquet}:file

cell_hulls

meta:map

${prefix}_cell-hulls.{csv,csv.gz,parquet}:file

gene_metadata

meta:map

${prefix}_gene-metadata.{csv,csv.gz,parquet}:file

metagene_rates

meta:map

${prefix}_metagene-rates.{csv,csv.gz,parquet}:file

metagene_loadings

meta:map

${prefix}_metagene-loadings.{csv,csv.gz,parquet}:file

cell_voxels

meta:map

${prefix}_cell-voxels.{csv,csv.gz,parquet}:file

versions_proseg

${task.process}:string

proseg:string

proseg --version | sed 's/proseg //':eval

Topics

versions

${task.process}:string

proseg:string

proseg --version | sed 's/proseg //':eval

Tools

proseg GPLv3

maintainers

get in touch

`meta`
`:map`

`transcripts`
`:file`

`mode`
`:string`

`transcript_metadata_fmt`
`:string`

`cell_metadata_fmt`
`:file`

`expected_counts_fmt`
`:file`

`zarr`

`meta`
`:map`

`${prefix}.zarr`
`:file`

`transcript_metadata`

`meta`
`:map`

`${prefix}_transcript-metadata.{csv,csv.gz,parquet}`
`:file`

`cell_polygons`

`meta`
`:map`

`${prefix}_cell-polygons.geojson.gz`
`:file`

`cell_metadata`

`meta`
`:map`

`${prefix}_cell-metadata.{csv,csv.gz,parquet}`
`:file`

`cell_polygons_layers`

`meta`
`:map`

`${prefix}_cell-polygons-layers.geojson.gz`
`:file`

`expected_counts`

`meta`
`:map`

`${prefix}_expected-counts.{csv,csv.gz,parquet}`
`:file`

`union_cell_polygons`

`meta`
`:map`

`${prefix}_cell-polygons-union.geojson.gz`
`:file`

`maxpost_counts`

`meta`
`:map`

`${prefix}_maxpost-counts.{csv,csv.gz,parquet}`
`:file`

`output_rates`

`meta`
`:map`

`${prefix}_output-rates.{csv,csv.gz,parquet}`
`:file`

`cell_hulls`

`meta`
`:map`

`${prefix}_cell-hulls.{csv,csv.gz,parquet}`
`:file`

`gene_metadata`

`meta`
`:map`

`${prefix}_gene-metadata.{csv,csv.gz,parquet}`
`:file`

`metagene_rates`

`meta`
`:map`

`${prefix}_metagene-rates.{csv,csv.gz,parquet}`
`:file`

`metagene_loadings`

`meta`
`:map`

`${prefix}_metagene-loadings.{csv,csv.gz,parquet}`
`:file`

`cell_voxels`

`meta`
`:map`

`${prefix}_cell-voxels.{csv,csv.gz,parquet}`
`:file`

`versions_proseg`

`${task.process}`
`:string`

`proseg`
`:string`

`proseg --version | sed 's/proseg //'`
`:eval`

`versions`

`${task.process}`
`:string`

`proseg`
`:string`

`proseg --version | sed 's/proseg //'`
`:eval`

proseg
GPLv3