Nextflow Registry | nf-core/bioformats2raw@0.0.0-6c4ed3a

nf-core/bioformats2raw @ 0.0.0-6c4ed3a

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: 0.0.0-6c4ed3a

Total downloads: 7

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:06:09 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbioformats2raw/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bioformats2raw/blobs/sha256:02929167ea926a3d72b1c72e261eef6cc53c3b4d84f03c14f3c87bc49030c325
Size	2.8 KB
Checksum	sha256:02929167ea926a3d72b1c72e261eef6cc53c3b4d84f03c14f3c87bc49030c325
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:06:09 (UTC)		4	2.8 KB
0.0.0-0c7146d	08 Apr 2026 18:47:41 (UTC)		3	2.8 KB