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Available transformation images reference

Each transformation image defines what input formats it accepts and what ODM objects it produces. Use GET /api/v1/transformations/images to retrieve the current list of available images and their versions.

metadata-basic

Note: The metadata-basic image was introduced as an example transformation.

Description: Basic converter from attachment to metadata.

Input formats: csv

Output formats: samples

Default memory: 256Mi

Default volume: 5Gi

Use case: Converts a CSV file attached to a study into an ODM Sample metadata group. On success, the image converts the CSV to TSV and automatically triggers ODM's multipart sample import, creating a new Sample group linked to the same study as the source attachment.

Example data field:

{
  "source": { "csv": {} },
  "destination": { "samples": {} }
}

For the end-to-end job workflow (create a configuration, submit a dry run, monitor, and review logs), see How to run a transformation.

hdf5-cells

Description: Import single-cell data and metadata from HDF5 format to ODM.

Input formats: H5AD (AnnData), 10x Genomics H5 (converted internally to H5AD before processing), Legacy 10x Genomics H5 v<3 (single-genome only; multi-genome legacy files are not supported).

Output formats: ODM Cell Group, Expression Group, with optional Sample, Library, and Preparation groups.

Default memory: 5Gi

Default volume: 5Gi

For a job using an H5AD inputs recommended volume_size is ≥ 1.4× the original file size.

When setting volume_size for a job using an H5 input file, allocate at least 4× the original attachment size (for example, a 5 GB file requires volume_size ≥ 20 GB). H5 inputs require additional scratch space because the transformation converts them to H5AD during processing.

For the full how-to and the data field schema, see the single-cell subsection.

Version conventions

  • latest is an alias for the most recent stable version of an image. Use it for exploration and development.
  • Specific tags (for example, 0.0.7) pin the job to a particular image version. Use them when you need to reproduce a previous result - the exact image and version used in any job are recorded in its logs.