Referencing genome files from a workflow definition - AWS HealthOmics

AWS HealthOmics variant stores and annotation stores will no longer be open to new customers starting November 7th, 2025. If you would like to use variant stores or annotation stores, sign up prior to that date. Existing customers can continue to use the service as normal. For more information, see AWS HealthOmics variant store and annotation store availability change.

Referencing genome files from a workflow definition

An HealthOmics reference store object can be referred to with a URI like the following. Use your own account ID, reference store ID, and reference ID where indicated.

omics://account ID.storage.us-west-2.amazonaws.com/reference store id/reference/id

Some workflows will require both the SOURCE and INDEX files for the reference genome. The previous URI is the default short form and will default to the SOURCE file. In order to specify either file, you can use the long URI form, as follows.

omics://account ID.storage.us-west-2.amazonaws.com/reference store id/reference/id/source
omics://account ID.storage.us-west-2.amazonaws.com/reference store id/reference/id/index

Using a sequence read set would have a similar pattern, as shown.

aws omics create-workflow \
     --name workflow name \
     --main sample workflow.wdl \
     --definition-uri omics://account ID.storage.us-west-2.amazonaws.com/sequence_store_id/readSet/id \
     --parameter-template file://parameters_sample_description.json

Some read sets, such as those based on FASTQ, can contain paired reads. In the following examples, they're referred to as SOURCE1 and SOURCE2. Formats such as BAM and CRAM will only have a SOURCE1 file. Some read sets will contain INDEX files such as bai or crai files. The preceding URI is the default short form and will default to the SOURCE1 file. To specify the exact file or index, you can use the long URI form, as follows.

omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>/source1
omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>/source2
omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>/index

The following is an example of an input JSON file that uses two Omics Storage URIs.

{
   "input_fasta": "omics://123456789012.storage.us-west-2.amazonaws.com/<reference_store_id>/reference/<id>",
   "input_cram": "omics://123456789012.storage.us-west-2.amazonaws.com/<sequence_store_id>/readSet/<id>"
}

Reference the input JSON file in the AWS CLI by adding --inputs file://<input_file.json> to your start-run request.