bioformats2raw module #7518
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bioformats2raw module #7518
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camlloyd
requested changes
Mar 3, 2025
| - image: | ||
| type: file | ||
| description: bioformats supported image file format | ||
| pattern: "*.{tif,tiff,svs,mrxs}" |
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Are there suitable ontologies you could add here?
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| bioformats2raw: \$(bioformats2raw --version |& sed '1!d ; s/bioformats2raw //') |
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Could you make the version start with a numeric character, rather than Version =?
I think it would also be helpful to emit the Bio-Formats and
NGFF specification versions here.
| - "*ome.zarr": | ||
| type: directory | ||
| description: OME-Zarr fileset for image data storage. Specification can be found at https://ngff.openmicroscopy.org/latest/#storage-format | ||
| pattern: "*{ome.zarr}" |
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Similarly are there ontologies you could add here?
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| """ | ||
| touch ${prefix}.ome.zarr |
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Should this be a file, or a directory?
camlloyd
reviewed
Mar 3, 2025
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| """ | ||
| bioformats2raw \\ |
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I see you used label 'process_single' above.
Out of interest did you try using --max-workers $task.cpus here?
camlloyd
reviewed
Mar 3, 2025
| description: Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. | ||
| keywords: | ||
| - zarr | ||
| - OME-NGFF |
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This needs to be all lower case.
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PR checklist
Closes #7422
versions.ymlfile.labelnew modules: bioformats2raw
I used now a seqera container: community.wave.seqera.io/library/bioformats2raw:0.9.4--3eec45888b3759e5
The tool is not in conda-forge or bioconda but from the ome channel ( open microscopy environment ) and i get errors from linting:
The environment.yml of the module bioformats2raw is not valid: 'ome' is not one of ['bioconda', 'conda-forge'].