Nextflow Registry | nf-core/bioformats2raw@0.0.0-0c7146d

nf-core/bioformats2raw @ 0.0.0-0c7146d

Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.

zarr ome-ngff imaging

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @CaroAMN

Maintainers: @CaroAMN

Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.

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

include { BIOFORMATS2RAW } from 'nf-core/bioformats2raw'

MIT License

Process

`Name`	`BIOFORMATS2RAW`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`image` file	bioformats supported image file format `*.{tif,tiff,svs,mrxs}`

Output 4 channels

#1 omezarr tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`*ome.zarr` directory	OME-Zarr fileset for image data storage. Specification can be found at https://ngff.openmicroscopy.org/latest/#storage-format `*{ome.zarr}`

#2 versions_ngff tuple

`${task.process}` string	The name of the process
`ngff` string	The name of the tool
`bioformats2raw --version \|& sed -n "3s/NGFF specification version = //p"` eval	The expression to obtain the version of the tool

#3 versions_bioformats tuple

`${task.process}` string	The name of the process
`bio-formats` string	The name of the tool
`bioformats2raw --version \|& sed -n "2s/Bio-Formats version = //p"` eval	The expression to obtain the version of the tool

#4 versions_bioformats2raw tuple

`${task.process}` string	The name of the process
`bioformats2raw` string	The name of the tool
`bioformats2raw --version \|& sed -n "1s/Version = //p"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
bioformats2raw	Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.	https://github.com/glencoesoftware/bioformats2raw

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:26:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbioformats2raw/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bioformats2raw/blobs/sha256:8c9d3f5203d969f0777f703e174b3638daaab6f9723dda5f91a3867bf2628972
Size	2.8 KB
Checksum	sha256:8c9d3f5203d969f0777f703e174b3638daaab6f9723dda5f91a3867bf2628972
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:26:55 (UTC)		1	2.8 KB	-