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Amazon Omics examples
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‎awscli/examples/omics/batch-delete-read-set.rst‎

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**To delete multiple read sets**
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The following ``batch-delete-read-set`` example deletes two read sets. ::
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aws omics batch-delete-read-set \
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--sequence-store-id 1234567890 \
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--ids 1234567890 0123456789
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If there is an error deleting any of the specified read sets, the service returns an error list. ::
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{
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"errors": [
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{
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"code": "",
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"id": "0123456789",
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"message": "The specified readset does not exist."
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}
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]
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}
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For more information, see `Omics Storage <https://docs.aws.amazon.com/omics/latest/dev/sequence-stores.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/cancel-annotation-import-job.rst‎

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**To cancel an annotation import job**
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The following ``cancel-annotation-import-job`` example cancels an annotation import job with ID ``04f57618-xmpl-4fd0-9349-e5a85aefb997``. ::
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aws omics cancel-annotation-import-job \
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--job-id 04f57618-xmpl-4fd0-9349-e5a85aefb997
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For more information, see `Omics Analytics <https://docs.aws.amazon.com/omics/latest/dev/omics-analytics.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/cancel-run.rst‎

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**To cancel a run**
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The following ``cancel-run`` example cancels a run with ID ``1234567``. ::
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aws omics cancel-run \
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--id 1234567
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For more information, see `Omics Workflows <https://docs.aws.amazon.com/omics/latest/dev/workflows.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/cancel-variant-import-job.rst‎

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**To cancel a variant import job**
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The following ``cancel-variant-import-job`` example cancels a variant import job with ID ``69cb65d6-xmpl-4a4a-9025-4565794b684e``. ::
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aws omics cancel-variant-import-job \
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--job-id 69cb65d6-xmpl-4a4a-9025-4565794b684e
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For more information, see `Omics Analytics <https://docs.aws.amazon.com/omics/latest/dev/omics-analytics.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/create-annotation-store.rst‎

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**Example 1: To create a VCF annotation store**
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The following ``create-annotation-store`` example creates a VCF format annotation store. ::
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aws omics create-annotation-store \
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--name my_ann_store \
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--store-format VCF \
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--reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890
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Output::
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{
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"creationTime": "2022-11-23T22:48:39.226492Z",
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"id": "0a91xmplc71f",
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"name": "my_ann_store",
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"reference": {
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"referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
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},
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"status": "CREATING",
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"storeFormat": "VCF"
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}
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**Example 2: To create a TSV annotation store**
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The following ``create-annotation-store`` example creates a TSV format annotation store. ::
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aws omics create-annotation-store \
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--name tsv_ann_store \
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--store-format TSV \
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--reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890 \
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--store-options file://tsv-store-options.json
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``tsv-store-options.json`` configures format options for annotations. ::
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{
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"tsvStoreOptions": {
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"annotationType": "CHR_START_END_ZERO_BASE",
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"formatToHeader": {
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"CHR": "chromosome",
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"START": "start",
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"END": "end"
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},
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"schema": [
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{
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"chromosome": "STRING"
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},
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{
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"start": "LONG"
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},
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{
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"end": "LONG"
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},
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{
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"name": "STRING"
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}
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]
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}
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}
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Output::
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{
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"creationTime": "2022-11-30T01:28:08.525586Z",
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"id": "861cxmpl96b0",
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"name": "tsv_ann_store",
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"reference": {
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"referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
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},
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"status": "CREATING",
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"storeFormat": "TSV",
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"storeOptions": {
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"tsvStoreOptions": {
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"annotationType": "CHR_START_END_ZERO_BASE",
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"formatToHeader": {
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"CHR": "chromosome",
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"END": "end",
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"START": "start"
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},
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"schema": [
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{
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"chromosome": "STRING"
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},
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{
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"start": "LONG"
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},
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{
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"end": "LONG"
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},
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{
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"name": "STRING"
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}
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]
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}
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}
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}
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For more information, see `Omics Analytics <https://docs.aws.amazon.com/omics/latest/dev/omics-analytics.html>`__ in the Amazon Omics Developer Guide.

‎awscli/examples/omics/create-reference-store.rst‎

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**To create a reference store**
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The following ``create-reference-store`` example creates a reference store ``my-ref-store``. ::
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aws omics create-reference-store \
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--name my-ref-store
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Output::
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{
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"arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
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"creationTime": "2022-11-22T22:13:25.947Z",
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"id": "1234567890",
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"name": "my-ref-store"
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}
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For more information, see `Omics Storage <https://docs.aws.amazon.com/omics/latest/dev/sequence-stores.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/create-run-group.rst‎

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**To create a run group**
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The following ``create-run-group`` example creates a run group named ``cram-converter``. ::
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aws omics create-run-group \
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--name cram-converter \
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--max-cpus 20 \
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--max-duration 600
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Output::
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{
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"arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
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"id": "1234567",
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"tags": {}
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}
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For more information, see `Omics Workflows <https://docs.aws.amazon.com/omics/latest/dev/workflows.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/create-sequence-store.rst‎

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**To create a sequence store**
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The following ``create-sequence-store`` example creates a sequence store. ::
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aws omics create-sequence-store \
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--name my-seq-store
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Output::
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{
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"arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890",
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"creationTime": "2022-11-23T01:24:33.629Z",
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"id": "1234567890",
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"name": "my-seq-store"
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}
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For more information, see `Omics Storage <https://docs.aws.amazon.com/omics/latest/dev/sequence-stores.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/create-variant-store.rst‎

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**To create a variant store**
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The following ``create-variant-store`` example creates a variant store named ``my_var_store``. ::
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aws omics create-variant-store \
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--name my_var_store \
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--reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890
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Output::
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{
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"creationTime": "2022-11-23T22:09:07.534499Z",
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"id": "02dexmplcfdd",
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"name": "my_var_store",
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"reference": {
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"referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
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},
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"status": "CREATING"
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}
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For more information, see `Omics Analytics <https://docs.aws.amazon.com/omics/latest/dev/omics-analytics.html>`__ in the *Amazon Omics Developer Guide*.

‎awscli/examples/omics/create-workflow.rst‎

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**To create a workflow**
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The following ``create-workflow`` example creates a WDL workflow. ::
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aws omics create-workflow \
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--name cram-converter \
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--engine WDL \
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--definition-zip fileb://workflow-crambam.zip \
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--parameter-template file://workflow-params.json
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``workflow-crambam.zip`` is a ZIP archive containing a workflow definition. ``workflow-params.json`` defines runtime parameters for the workflow. ::
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{
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"ref_fasta" : {
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"description": "Reference genome fasta file",
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"optional": false
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},
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"ref_fasta_index" : {
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"description": "Index of the reference genome fasta file",
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"optional": false
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},
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"ref_dict" : {
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"description": "dictionary file for 'ref_fasta'",
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"optional": false
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},
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"input_cram" : {
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"description": "The Cram file to convert to BAM",
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"optional": false
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},
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"sample_name" : {
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"description": "The name of the input sample, used to name the output BAM",
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"optional": false
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}
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}
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Output::
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{
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"arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
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"id": "1234567",
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"status": "CREATING",
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"tags": {}
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}
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For more information, see `Omics Workflows <https://docs.aws.amazon.com/omics/latest/dev/workflows.html>`__ in the *Amazon Omics Developer Guide*.

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