Nextflow Registry | nf-core/proseg/proseg_to

nf-core/proseg/proseg_to_baysor @ 0.0.0-6c4ed3a

Convert proseg outputs to baysor format for import to Xenium explorer

segmentation spatial transcriptomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @derrik-gratz

Maintainers: @derrik-gratz

Convert proseg outputs to baysor format for import to Xenium explorer

Add the following snippet to your workflow script to include this module.

include { PROSEG_TO_BAYSOR } from 'nf-core/proseg/proseg_to_baysor'

MIT License

Process

`Name`	`PROSEG_TO_BAYSOR`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information
`transcript_metadata` file	Transcript ids, genes, revised positions, assignment probability, etc. `*transcript-metadata.csv.gz`

#2 tuple

`meta2` map	Groovy Map containing sample information
`cell_polygons` file	Path to the cell polygons file. `*cell-polygons.geojson.gz`

Output 3 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 baysor_cell_polygons tuple

`meta` map	Groovy Map containing sample information
`*baysor-cell-polygons.geojson` file	Path to the cell polygons file. `*baysor-cell-polygons.geojson`

#3 baysor_transcript_metadata tuple

`meta` map	Groovy Map containing sample information
`*baysor-transcript-metadata.csv` file	Transcript ids, genes, revised positions, assignment probability, etc. `*baysor-transcript-metadata.csv`

Tool	Description	Homepage
proseg	Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.	https://github.com/dcjones/proseg

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:38:41 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fproseg%2Fproseg_to_baysor/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/proseg/proseg_to_baysor/blobs/sha256:7cd47670fa28ce6ce0d41a90ba19a8d253009a5df3237e18ba2a07ae606627d0
Size	2.6 KB
Checksum	sha256:7cd47670fa28ce6ce0d41a90ba19a8d253009a5df3237e18ba2a07ae606627d0
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:38:41 (UTC)		3	2.6 KB
0.0.0-0c7146d	08 Apr 2026 19:28:46 (UTC)		4	2.6 KB