From dfae263d54c1738974905a89cb665d7c6767f34a Mon Sep 17 00:00:00 2001 From: Barry Devlin Date: Wed, 23 Jul 2025 10:06:03 -0700 Subject: [PATCH] Updates to workflow examples --- .../examples/omics/batch-delete-read-set.rst | 2 +- .../omics/cancel-annotation-import-job.rst | 2 +- .../omics/cancel-variant-import-job.rst | 2 +- .../omics/create-annotation-store.rst | 2 +- .../examples/omics/create-reference-store.rst | 2 +- awscli/examples/omics/create-run-cache.rst | 17 ++++ awscli/examples/omics/create-run-group.rst | 4 +- .../examples/omics/create-sequence-store.rst | 2 +- .../examples/omics/create-variant-store.rst | 2 +- awscli/examples/omics/create-workflow.rst | 1 + .../omics/delete-annotation-store.rst | 2 +- .../examples/omics/delete-reference-store.rst | 2 +- awscli/examples/omics/delete-reference.rst | 2 +- awscli/examples/omics/delete-run-cache.rst | 8 ++ .../examples/omics/delete-sequence-store.rst | 2 +- .../examples/omics/delete-variant-store.rst | 2 +- .../omics/get-annotation-import-job.rst | 2 +- .../examples/omics/get-annotation-store.rst | 2 +- .../omics/get-read-set-activation-job.rst | 2 +- .../omics/get-read-set-export-job.rst | 2 +- .../omics/get-read-set-import-job.rst | 2 +- .../examples/omics/get-read-set-metadata.rst | 2 +- awscli/examples/omics/get-read-set.rst | 2 +- .../omics/get-reference-import-job.rst | 2 +- .../examples/omics/get-reference-metadata.rst | 2 +- awscli/examples/omics/get-reference-store.rst | 2 +- awscli/examples/omics/get-reference.rst | 2 +- awscli/examples/omics/get-run-cache.rst | 19 +++++ awscli/examples/omics/get-run-task.rst | 22 ++--- awscli/examples/omics/get-sequence-store.rst | 2 +- .../examples/omics/get-variant-import-job.rst | 2 +- awscli/examples/omics/get-variant-store.rst | 2 +- .../omics/list-annotation-import-jobs.rst | 2 +- .../examples/omics/list-annotation-stores.rst | 2 +- .../omics/list-read-set-activation-jobs.rst | 2 +- .../omics/list-read-set-export-jobs.rst | 2 +- .../omics/list-read-set-import-jobs.rst | 2 +- awscli/examples/omics/list-read-sets.rst | 2 +- .../omics/list-reference-import-jobs.rst | 2 +- .../examples/omics/list-reference-stores.rst | 2 +- awscli/examples/omics/list-references.rst | 2 +- awscli/examples/omics/list-run-caches.rst | 30 +++++++ .../examples/omics/list-sequence-stores.rst | 2 +- .../examples/omics/list-tags-for-resource.rst | 2 +- .../omics/list-variant-import-jobs.rst | 2 +- awscli/examples/omics/list-variant-stores.rst | 2 +- .../omics/start-annotation-import-job.rst | 2 +- .../omics/start-read-set-activation-job.rst | 2 +- .../omics/start-read-set-export-job.rst | 2 +- .../omics/start-read-set-import-job.rst | 2 +- .../omics/start-reference-import-job.rst | 2 +- awscli/examples/omics/start-run.rst | 84 ++++++++++++++++++- .../omics/start-variant-import-job.rst | 2 +- awscli/examples/omics/tag-resource.rst | 2 +- awscli/examples/omics/untag-resource.rst | 2 +- .../omics/update-annotation-store.rst | 2 +- awscli/examples/omics/update-run-cache.rst | 9 ++ awscli/examples/omics/update-run-group.rst | 15 +--- .../examples/omics/update-variant-store.rst | 2 +- awscli/examples/omics/wait.rst | 2 +- 60 files changed, 230 insertions(+), 79 deletions(-) create mode 100644 awscli/examples/omics/create-run-cache.rst create mode 100644 awscli/examples/omics/delete-run-cache.rst create mode 100644 awscli/examples/omics/get-run-cache.rst create mode 100644 awscli/examples/omics/list-run-caches.rst create mode 100644 awscli/examples/omics/update-run-cache.rst diff --git a/awscli/examples/omics/batch-delete-read-set.rst b/awscli/examples/omics/batch-delete-read-set.rst index 50865de718df..3a2d66bac67f 100644 --- a/awscli/examples/omics/batch-delete-read-set.rst +++ b/awscli/examples/omics/batch-delete-read-set.rst @@ -18,4 +18,4 @@ If there is an error deleting any of the specified read sets, the service return ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/cancel-annotation-import-job.rst b/awscli/examples/omics/cancel-annotation-import-job.rst index 815515269364..a473560c0fe6 100644 --- a/awscli/examples/omics/cancel-annotation-import-job.rst +++ b/awscli/examples/omics/cancel-annotation-import-job.rst @@ -5,4 +5,4 @@ The following ``cancel-annotation-import-job`` example cancels an annotation imp aws omics cancel-annotation-import-job \ --job-id 04f57618-xmpl-4fd0-9349-e5a85aefb997 -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/cancel-variant-import-job.rst b/awscli/examples/omics/cancel-variant-import-job.rst index c085ce422749..7d2474d79255 100644 --- a/awscli/examples/omics/cancel-variant-import-job.rst +++ b/awscli/examples/omics/cancel-variant-import-job.rst @@ -5,4 +5,4 @@ The following ``cancel-variant-import-job`` example cancels a variant import job aws omics cancel-variant-import-job \ --job-id 69cb65d6-xmpl-4a4a-9025-4565794b684e -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/create-annotation-store.rst b/awscli/examples/omics/create-annotation-store.rst index 88da14afd87a..fa59fef2b5d9 100644 --- a/awscli/examples/omics/create-annotation-store.rst +++ b/awscli/examples/omics/create-annotation-store.rst @@ -94,4 +94,4 @@ Output:: } } -For more information, see `Omics Analytics `__ in the Amazon Omics Developer Guide. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/create-reference-store.rst b/awscli/examples/omics/create-reference-store.rst index 627b0764b834..d9d7c0694e24 100644 --- a/awscli/examples/omics/create-reference-store.rst +++ b/awscli/examples/omics/create-reference-store.rst @@ -14,4 +14,4 @@ Output:: "name": "my-ref-store" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/create-run-cache.rst b/awscli/examples/omics/create-run-cache.rst new file mode 100644 index 000000000000..929966ffe73b --- /dev/null +++ b/awscli/examples/omics/create-run-cache.rst @@ -0,0 +1,17 @@ +**To create a run cache** + +The following ``create-run-cache`` example creates a run cache with a specified S3 location for storing the cached task outputs. :: + + aws omics create-run-cache \ + --cache-s3-location "s3://example-bucket/cache/" + +Output:: + + { + "arn": "arn:aws:omics:us-west-2:123456789012:runCache/1234567", + "id": "1234567", + "status": "ACTIVE", + "tags": {} + } + +For more information, see `Creating a run cache `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/create-run-group.rst b/awscli/examples/omics/create-run-group.rst index 3e7a4002b1a4..aec5a707f859 100644 --- a/awscli/examples/omics/create-run-group.rst +++ b/awscli/examples/omics/create-run-group.rst @@ -5,9 +5,7 @@ The following ``create-run-group`` example creates a run group named ``cram-conv aws omics create-run-group \ --name cram-converter \ --max-cpus 20 \ - --max-gpus 10 \ - --max-duration 600 \ - --max-runs 5 + --max-duration 600 Output:: diff --git a/awscli/examples/omics/create-sequence-store.rst b/awscli/examples/omics/create-sequence-store.rst index 7b2dd19a233f..2eadbf73bb54 100644 --- a/awscli/examples/omics/create-sequence-store.rst +++ b/awscli/examples/omics/create-sequence-store.rst @@ -14,4 +14,4 @@ Output:: "name": "my-seq-store" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/create-variant-store.rst b/awscli/examples/omics/create-variant-store.rst index 44461a126cb1..9423ba27d4fa 100644 --- a/awscli/examples/omics/create-variant-store.rst +++ b/awscli/examples/omics/create-variant-store.rst @@ -18,4 +18,4 @@ Output:: "status": "CREATING" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/create-workflow.rst b/awscli/examples/omics/create-workflow.rst index bcaf693666a9..40e6017d4e5a 100644 --- a/awscli/examples/omics/create-workflow.rst +++ b/awscli/examples/omics/create-workflow.rst @@ -40,6 +40,7 @@ Output:: "id": "1234567", "status": "CREATING", "tags": {} + "uuid": "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" } For more information, see `Creating private workflows `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/delete-annotation-store.rst b/awscli/examples/omics/delete-annotation-store.rst index a03a54cf945d..7420cf211f74 100644 --- a/awscli/examples/omics/delete-annotation-store.rst +++ b/awscli/examples/omics/delete-annotation-store.rst @@ -11,4 +11,4 @@ Output:: "status": "DELETING" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/delete-reference-store.rst b/awscli/examples/omics/delete-reference-store.rst index 461ea16fb3c3..3fc62ed8a48c 100644 --- a/awscli/examples/omics/delete-reference-store.rst +++ b/awscli/examples/omics/delete-reference-store.rst @@ -5,4 +5,4 @@ The following ``delete-reference-store`` example deletes a reference store with aws omics delete-reference-store \ --id 1234567890 -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/delete-reference.rst b/awscli/examples/omics/delete-reference.rst index d6aa8ec0c5c1..5fad2dcfb025 100644 --- a/awscli/examples/omics/delete-reference.rst +++ b/awscli/examples/omics/delete-reference.rst @@ -6,4 +6,4 @@ The following ``delete-reference`` example deletes a reference. :: --reference-store-id 1234567890 \ --id 1234567890 -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/delete-run-cache.rst b/awscli/examples/omics/delete-run-cache.rst new file mode 100644 index 000000000000..481fe3399420 --- /dev/null +++ b/awscli/examples/omics/delete-run-cache.rst @@ -0,0 +1,8 @@ +**To delete a run cache** + +The following ``delete-run-cache`` example deletes the run cache ``1234567``. :: + + aws omics delete-run-cache \ + --id "1234567" \ + +For more information, see `Deleting a run cache `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/delete-sequence-store.rst b/awscli/examples/omics/delete-sequence-store.rst index 8b009b16289a..96715a1c1583 100644 --- a/awscli/examples/omics/delete-sequence-store.rst +++ b/awscli/examples/omics/delete-sequence-store.rst @@ -5,4 +5,4 @@ The following ``delete-sequence-store`` example deletes a sequence store with ID aws omics delete-sequence-store \ --id 1234567890 -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/delete-variant-store.rst b/awscli/examples/omics/delete-variant-store.rst index 948d7d51136b..f980f90133cd 100644 --- a/awscli/examples/omics/delete-variant-store.rst +++ b/awscli/examples/omics/delete-variant-store.rst @@ -11,4 +11,4 @@ Output:: "status": "DELETING" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-annotation-import-job.rst b/awscli/examples/omics/get-annotation-import-job.rst index 98ff9d06ec26..26dac35f7398 100644 --- a/awscli/examples/omics/get-annotation-import-job.rst +++ b/awscli/examples/omics/get-annotation-import-job.rst @@ -23,4 +23,4 @@ Output:: "updateTime": "2022-11-30T01:42:39.134009Z" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-annotation-store.rst b/awscli/examples/omics/get-annotation-store.rst index 269082a5f7cd..5a2d92945be4 100644 --- a/awscli/examples/omics/get-annotation-store.rst +++ b/awscli/examples/omics/get-annotation-store.rst @@ -21,4 +21,4 @@ Output:: "tags": {} } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-read-set-activation-job.rst b/awscli/examples/omics/get-read-set-activation-job.rst index 196e7c67f5b5..9d3dee108e78 100644 --- a/awscli/examples/omics/get-read-set-activation-job.rst +++ b/awscli/examples/omics/get-read-set-activation-job.rst @@ -24,4 +24,4 @@ Output:: "statusMessage": "The job completed successfully." } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-read-set-export-job.rst b/awscli/examples/omics/get-read-set-export-job.rst index bbf5d07a446b..378f126a2ce8 100644 --- a/awscli/examples/omics/get-read-set-export-job.rst +++ b/awscli/examples/omics/get-read-set-export-job.rst @@ -18,4 +18,4 @@ Output:: "statusMessage": "The job is submitted and will start soon." } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-read-set-import-job.rst b/awscli/examples/omics/get-read-set-import-job.rst index 3c8d9811c62d..ba71f49c6fce 100644 --- a/awscli/examples/omics/get-read-set-import-job.rst +++ b/awscli/examples/omics/get-read-set-import-job.rst @@ -70,4 +70,4 @@ Output:: "statusMessage": "The job is currently in progress." } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-read-set-metadata.rst b/awscli/examples/omics/get-read-set-metadata.rst index 0153cf341734..b670f1829cb1 100644 --- a/awscli/examples/omics/get-read-set-metadata.rst +++ b/awscli/examples/omics/get-read-set-metadata.rst @@ -38,4 +38,4 @@ Output:: "subjectId": "fastq-subject" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-read-set.rst b/awscli/examples/omics/get-read-set.rst index bbe3a9b10ec7..a6ba5a68f017 100644 --- a/awscli/examples/omics/get-read-set.rst +++ b/awscli/examples/omics/get-read-set.rst @@ -7,4 +7,4 @@ The following ``get-read-set`` example downloads part 3 of a read set as ``12345 --id 1234567890 \ --part-number 3 1234567890.3.bam -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. \ No newline at end of file diff --git a/awscli/examples/omics/get-reference-import-job.rst b/awscli/examples/omics/get-reference-import-job.rst index b82a5aa255da..5fd978f1d46a 100644 --- a/awscli/examples/omics/get-reference-import-job.rst +++ b/awscli/examples/omics/get-reference-import-job.rst @@ -25,4 +25,4 @@ Output:: "statusMessage": "The job is currently in progress." } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-reference-metadata.rst b/awscli/examples/omics/get-reference-metadata.rst index 74b05ae836cf..912a7540a883 100644 --- a/awscli/examples/omics/get-reference-metadata.rst +++ b/awscli/examples/omics/get-reference-metadata.rst @@ -31,4 +31,4 @@ Output:: "updateTime": "2022-11-22T22:27:09.033Z" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-reference-store.rst b/awscli/examples/omics/get-reference-store.rst index 67b04350a982..50c921c2ae26 100644 --- a/awscli/examples/omics/get-reference-store.rst +++ b/awscli/examples/omics/get-reference-store.rst @@ -14,4 +14,4 @@ Output:: "name": "my-rstore-0" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-reference.rst b/awscli/examples/omics/get-reference.rst index 9cb1de7e472f..22343638909d 100644 --- a/awscli/examples/omics/get-reference.rst +++ b/awscli/examples/omics/get-reference.rst @@ -7,4 +7,4 @@ The following ``get-reference`` example downloads part 1 of a genome as ``hg38.1 --id 1234567890 \ --part-number 1 hg38.1.fa -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-run-cache.rst b/awscli/examples/omics/get-run-cache.rst new file mode 100644 index 000000000000..a55dd88f45bc --- /dev/null +++ b/awscli/examples/omics/get-run-cache.rst @@ -0,0 +1,19 @@ +**To view a run cache** + +The following ``get-run-cache`` example retrieves metadata for the run cache ``1234567``. :: + + aws omics get-run-cache --id 1234567 + +Output:: + + { + "arn": "arn:aws:omics:us-west-2:123456789012:runCache/1234567", + "cacheBehavior": "CACHE_ON_FAILURE", + "cacheS3Uri": "s3://omics-output-us-west-2-123456789012/cache/decbe15f-2b59-88bb-6c6d-2759000b90a1/", + "creationTime": "2025-06-30T21:29:03.406500+00:00", + "id": "1234567", + "status": "ACTIVE", + "tags": {} + } + +For more information, see `Contents of a run cache `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-run-task.rst b/awscli/examples/omics/get-run-task.rst index 9f09c4476104..d3932528de83 100644 --- a/awscli/examples/omics/get-run-task.rst +++ b/awscli/examples/omics/get-run-task.rst @@ -3,21 +3,23 @@ The following ``get-run-task`` example gets details about a workflow task. :: aws omics get-run-task \ - --id 1234567 \ - --task-id 1234567 + --id "6096280" \ + --task-id "6657068" Output:: { - "cpus": 1, - "creationTime": "2022-11-30T23:13:00.718651Z", - "logStream": "arn:aws:logs:us-west-2:123456789012:log-group:/aws/omics/WorkflowLog:log-stream:run/1234567/task/1234567", - "memory": 15, - "name": "CramToBamTask", - "startTime": "2022-11-30T23:17:47.016Z", + "taskId": "6657068", "status": "COMPLETED", - "stopTime": "2022-11-30T23:18:21.503Z", - "taskId": "1234567" + "name": "FileCopy", + "cpus": 1, + "memory": 1, + "creationTime": "2025-06-30T23:14:54.329480+00:00", + "startTime": "2025-06-30T23:17:43.437000+00:00", + "stopTime": "2025-06-30T23:17:57.662000+00:00", + "logStream": "arn:aws:logs:us-west-2:123456789012:log-group:/aws/omics/WorkflowLog:log-stream:run/6096280/task/6657068", + "gpus": 0, + "instanceType": "omics.c.large" } For more information, see `Task lifecycle in a HealthOmics run `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-sequence-store.rst b/awscli/examples/omics/get-sequence-store.rst index d87a83f8d54d..d597eee9a806 100644 --- a/awscli/examples/omics/get-sequence-store.rst +++ b/awscli/examples/omics/get-sequence-store.rst @@ -14,4 +14,4 @@ Output:: "name": "my-seq-store" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-variant-import-job.rst b/awscli/examples/omics/get-variant-import-job.rst index 2728f9d5a5f8..69977cf3db15 100644 --- a/awscli/examples/omics/get-variant-import-job.rst +++ b/awscli/examples/omics/get-variant-import-job.rst @@ -23,4 +23,4 @@ Output:: "updateTime": "2022-11-23T22:43:05.898309Z" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/get-variant-store.rst b/awscli/examples/omics/get-variant-store.rst index d1cca2baffee..a9f1cbe2f70d 100644 --- a/awscli/examples/omics/get-variant-store.rst +++ b/awscli/examples/omics/get-variant-store.rst @@ -21,4 +21,4 @@ Output:: "updateTime": "2022-11-23T22:09:24.931711Z" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-annotation-import-jobs.rst b/awscli/examples/omics/list-annotation-import-jobs.rst index 9a3a5aeaa03e..b36f8cffa05a 100644 --- a/awscli/examples/omics/list-annotation-import-jobs.rst +++ b/awscli/examples/omics/list-annotation-import-jobs.rst @@ -29,4 +29,4 @@ Output:: ] } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-annotation-stores.rst b/awscli/examples/omics/list-annotation-stores.rst index 64b7158bc77f..b79fb612dd83 100644 --- a/awscli/examples/omics/list-annotation-stores.rst +++ b/awscli/examples/omics/list-annotation-stores.rst @@ -25,4 +25,4 @@ Output:: ] } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-read-set-activation-jobs.rst b/awscli/examples/omics/list-read-set-activation-jobs.rst index 490f951493b2..0734c932c759 100644 --- a/awscli/examples/omics/list-read-set-activation-jobs.rst +++ b/awscli/examples/omics/list-read-set-activation-jobs.rst @@ -25,4 +25,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-read-set-export-jobs.rst b/awscli/examples/omics/list-read-set-export-jobs.rst index a6849e9e8933..27fb2cbcc0e1 100644 --- a/awscli/examples/omics/list-read-set-export-jobs.rst +++ b/awscli/examples/omics/list-read-set-export-jobs.rst @@ -27,4 +27,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-read-set-import-jobs.rst b/awscli/examples/omics/list-read-set-import-jobs.rst index bf187242794b..76be18e531ad 100644 --- a/awscli/examples/omics/list-read-set-import-jobs.rst +++ b/awscli/examples/omics/list-read-set-import-jobs.rst @@ -28,4 +28,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-read-sets.rst b/awscli/examples/omics/list-read-sets.rst index bc253da0c2ea..c53e1e00efeb 100644 --- a/awscli/examples/omics/list-read-sets.rst +++ b/awscli/examples/omics/list-read-sets.rst @@ -24,4 +24,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-reference-import-jobs.rst b/awscli/examples/omics/list-reference-import-jobs.rst index 62dfec741e09..17551894ad6b 100644 --- a/awscli/examples/omics/list-reference-import-jobs.rst +++ b/awscli/examples/omics/list-reference-import-jobs.rst @@ -27,4 +27,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-reference-stores.rst b/awscli/examples/omics/list-reference-stores.rst index b8ced6fdffa6..1a0e2ac89b95 100644 --- a/awscli/examples/omics/list-reference-stores.rst +++ b/awscli/examples/omics/list-reference-stores.rst @@ -17,4 +17,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-references.rst b/awscli/examples/omics/list-references.rst index 519df2bedfe3..4346fb59d5a6 100644 --- a/awscli/examples/omics/list-references.rst +++ b/awscli/examples/omics/list-references.rst @@ -22,4 +22,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-run-caches.rst b/awscli/examples/omics/list-run-caches.rst new file mode 100644 index 000000000000..66e281de35e1 --- /dev/null +++ b/awscli/examples/omics/list-run-caches.rst @@ -0,0 +1,30 @@ +**To get a list of run caches** + +The following ``list-run-caches`` example lists all existing run caches in the associated AWS HealthOmics account. :: + + aws omics list-run-caches + +Output:: + + { + "items": [ + { + "arn": "arn:aws:omics:us-west-2:123456789012:runCache/2743932", + "cacheBehavior": "CACHE_ON_FAILURE", + "cacheS3Uri": "s3://omics-output-us-west-2-123456789012/cache/decbe15f-2b59-88bb-6c6d-2759000b90a1/", + "creationTime": "2025-06-30T21:29:03.406500+00:00", + "id": "2743932", + "status": "ACTIVE" + }, + { + "arn": "arn:aws:omics:us-west-2:123456789012:runCache/7038070", + "cacheBehavior": "CACHE_ON_FAILURE", + "cacheS3Uri": "s3://omics-output-us-west-2-123456789012/cache/30cbe158-d6cd-6e9e-2cf1-9e40ff641318/", + "creationTime": "2025-06-30T21:15:13.683730+00:00", + "id": "7038070", + "status": "ACTIVE" + }, + ] + } + +For more information, see `Call caching for HealthOmics runs `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-sequence-stores.rst b/awscli/examples/omics/list-sequence-stores.rst index c0324b6af4c4..91c35b0a2122 100644 --- a/awscli/examples/omics/list-sequence-stores.rst +++ b/awscli/examples/omics/list-sequence-stores.rst @@ -17,4 +17,4 @@ Output:: ] } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-tags-for-resource.rst b/awscli/examples/omics/list-tags-for-resource.rst index f852cc0bdc1a..39bfb2bd320c 100644 --- a/awscli/examples/omics/list-tags-for-resource.rst +++ b/awscli/examples/omics/list-tags-for-resource.rst @@ -13,4 +13,4 @@ Output:: } } -For more information, see `Tagging resources in Amazon Omics `__ in the *Amazon Omics Developer Guide*. +For more information, see `Tagging resources in AWS HealthOmics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-variant-import-jobs.rst b/awscli/examples/omics/list-variant-import-jobs.rst index 1c9fb9ed8ffa..1064688f4272 100644 --- a/awscli/examples/omics/list-variant-import-jobs.rst +++ b/awscli/examples/omics/list-variant-import-jobs.rst @@ -29,4 +29,4 @@ Output:: ] } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/list-variant-stores.rst b/awscli/examples/omics/list-variant-stores.rst index 092f8dd4e3dd..64e7e6fdea94 100644 --- a/awscli/examples/omics/list-variant-stores.rst +++ b/awscli/examples/omics/list-variant-stores.rst @@ -32,4 +32,4 @@ Output:: ] } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/start-annotation-import-job.rst b/awscli/examples/omics/start-annotation-import-job.rst index b5c5a04b2b00..4a355706a300 100644 --- a/awscli/examples/omics/start-annotation-import-job.rst +++ b/awscli/examples/omics/start-annotation-import-job.rst @@ -14,4 +14,4 @@ Output:: "jobId": "984162c7-xmpl-4d23-ab47-286f7950bfbf" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/start-read-set-activation-job.rst b/awscli/examples/omics/start-read-set-activation-job.rst index dab0c5b8addb..2d7f80df6859 100644 --- a/awscli/examples/omics/start-read-set-activation-job.rst +++ b/awscli/examples/omics/start-read-set-activation-job.rst @@ -15,4 +15,4 @@ Output:: "status": "SUBMITTED" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide**. diff --git a/awscli/examples/omics/start-read-set-export-job.rst b/awscli/examples/omics/start-read-set-export-job.rst index a33be5c76921..2891e1fc9c8b 100644 --- a/awscli/examples/omics/start-read-set-export-job.rst +++ b/awscli/examples/omics/start-read-set-export-job.rst @@ -19,4 +19,4 @@ Output:: "status": "SUBMITTED" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/start-read-set-import-job.rst b/awscli/examples/omics/start-read-set-import-job.rst index 7626e392add3..f8af7a6e9f71 100644 --- a/awscli/examples/omics/start-read-set-import-job.rst +++ b/awscli/examples/omics/start-read-set-import-job.rst @@ -34,4 +34,4 @@ Output:: } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/start-reference-import-job.rst b/awscli/examples/omics/start-reference-import-job.rst index 491e14c5dd17..89094653bf90 100644 --- a/awscli/examples/omics/start-reference-import-job.rst +++ b/awscli/examples/omics/start-reference-import-job.rst @@ -17,4 +17,4 @@ Output:: "status": "SUBMITTED" } -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Storage `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/start-run.rst b/awscli/examples/omics/start-run.rst index 64caa29b24e9..473a35c25f0a 100644 --- a/awscli/examples/omics/start-run.rst +++ b/awscli/examples/omics/start-run.rst @@ -29,14 +29,92 @@ Output:: "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567", "id": "1234567", "status": "PENDING", - "tags": {} + "tags": {}, + "uuid": "12345678-1234-1234-1234-123456789012", + "runOutputUri": "s3://omics-output-bucket/workflow-results/" } +**To run a shared workflow** + +The following example demonstrates how to use ``start-run`` with a shared workflow. :: + + aws omics start-run \ + --workflow-id 1234567 \ + --workflow-owner-id 123456789012 \ + --role-arn arn:aws:iam::123456789012:role/HealthOmicsServiceRole \ + --output-uri s3://your-bucket/results/ \ + --parameters '{ + "param1": "value1", + "param2": "value2" + }' + +Output:: + + { + "arn": "arn:aws:omics:us-east-1:123456789012:run/1234567", + "id": "1234567", + "status": "PENDING", + "tags": {}, + "uuid": "a1b2c3d4-5e6f-7g8h-9i0j-1k2l3m4n5o6p", + "runOutputUri": "s3://your-bucket/results/1234567" + } + +**To run a workflow with call caching enabled** + +The following example demonstrates how to use ``start-run`` with call caching enabled. :: + + aws omics start-run \ + --workflow-id 7206765 \ + --role-arn arn:aws:iam::123456789012:role/HealthOmicsServiceRole \ + --output-uri s3://healthomics-output-bucket-demo/results/ \ + --parameters '{ + "input": "s3://healthomics-output-bucket-demo/input/samplesheet.csv", + "protocol": "10XV3", + "ecr_registry": "123456789012.dkr.ecr.us-east-1.amazonaws.com", + "gtf": "s3://healthomics-output-bucket-demo/reference/genes.gtf", + "aligner": "star", + "fasta": "s3://healthomics-output-bucket-demo/reference/genome.fa", + "skip_emptydrops": "true" + }' \ + --cache-id 1234567 \ + --cache-behavior "CACHE_ALWAYS" + +Output:: + + { + "arn": "arn:aws:omics:us-east-1:123456789012:run/3282892", + "id": "3282892", + "status": "PENDING", + "tags": {}, + "uuid": "b8cbfb50-64f7-359a-443a-24ed14c4d9e8", + "runOutputUri": "s3://healthomics-output-bucket-demo/results/3282892" + } + +**To duplicate a run** + +The following example demonstrates how to use ``start-run`` to duplicate a run with ID ``3282892``. :: + + aws omics start-run \ + --role-arn arn:aws:iam::713632817814:role/HealthOmicsServiceRole \ + --output-uri s3://healthomics-output-bucket-demo/results/ \ + --run-id 3282892 + +Output:: + + { + "arn": "arn:aws:omics:us-east-1:713632817814:run/6037016", + "id": "6037016", + "status": "PENDING", + "tags": {}, + "uuid": "a0cc0766-def1-cc71-8dc4-1300d3e64f90", + "runOutputUri": "s3://healthomics-output-bucket-demo/results/6037016" + } + For more information, see `Starting a run `__ in the *AWS HealthOmics User Guide*. -**To load source files from Amazon Omics** +**To load source files from AWS HealthOmics** -You can also load source files from Amazon Omics storage, by using service-specific URIs. The following example `workflow-inputs.json` file uses Amazon Omics URIs for read set and reference genome sources. :: +You can also load source files from AWS HealthOmics storage, by using service-specific URIs. The following example `workflow-inputs.json` file uses AWS HealthOmics URIs for read set and reference genome sources. :: { "sample_name": "NA12878", diff --git a/awscli/examples/omics/start-variant-import-job.rst b/awscli/examples/omics/start-variant-import-job.rst index c5e9bcbe3aee..3f1a40bf8e5c 100644 --- a/awscli/examples/omics/start-variant-import-job.rst +++ b/awscli/examples/omics/start-variant-import-job.rst @@ -14,4 +14,4 @@ Output:: "jobId": "edd7b8ce-xmpl-47e2-bc99-258cac95a508" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/tag-resource.rst b/awscli/examples/omics/tag-resource.rst index 955c085dc636..c96fd53f11b3 100644 --- a/awscli/examples/omics/tag-resource.rst +++ b/awscli/examples/omics/tag-resource.rst @@ -6,4 +6,4 @@ The following ``tag-resource`` example adds a ``department`` tag to a workflow w --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567 \ --tags department=analytics -For more information, see `Tagging resources in Amazon Omics `__ in the *Amazon Omics Developer Guide*. +For more information, see `Tagging resources in AWS HealthOmics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/untag-resource.rst b/awscli/examples/omics/untag-resource.rst index 73cc0e542cf7..4a816cd9168f 100644 --- a/awscli/examples/omics/untag-resource.rst +++ b/awscli/examples/omics/untag-resource.rst @@ -6,4 +6,4 @@ The following ``untag-resource`` example removes the ``department`` tag from a w --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567 \ --tag-keys department -For more information, see `Omics Storage `__ in the *Amazon Omics Developer Guide*. +For more information, see `Removing tags from a data store `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/update-annotation-store.rst b/awscli/examples/omics/update-annotation-store.rst index 58e7b18313b5..e9177ecca7bf 100644 --- a/awscli/examples/omics/update-annotation-store.rst +++ b/awscli/examples/omics/update-annotation-store.rst @@ -21,4 +21,4 @@ Output:: "updateTime": "2022-12-05T18:13:16.100051Z" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/update-run-cache.rst b/awscli/examples/omics/update-run-cache.rst new file mode 100644 index 000000000000..74cf4199f415 --- /dev/null +++ b/awscli/examples/omics/update-run-cache.rst @@ -0,0 +1,9 @@ +**To update a run cache** + +The following ``update-run-cache`` example updates a run cache with the new name ``updated-cache-name``. :: + + aws omics update-run-cache \ + --id "1234567" \ + --name "updated-cache-name" \ + +For more information, see `Updating a run cache `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/update-run-group.rst b/awscli/examples/omics/update-run-group.rst index 311a4e20b035..00f1c643df01 100644 --- a/awscli/examples/omics/update-run-group.rst +++ b/awscli/examples/omics/update-run-group.rst @@ -5,17 +5,6 @@ The following ``update-run-group`` example updates the settings of a run group w aws omics update-run-group \ --id 1234567 \ --max-cpus 10 + --name "updated-run-name" -Output:: - - { - "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567", - "creationTime": "2022-12-01T00:58:42.915219Z", - "id": "1234567", - "maxCpus": 10, - "maxDuration": 600, - "name": "cram-convert", - "tags": {} - } - -For more information, see `Omics Workflows `__ in the *Amazon Omics Developer Guide*. +For more information, see `Creating run groups `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/update-variant-store.rst b/awscli/examples/omics/update-variant-store.rst index 3af1aa9ee52f..bd3ee4336b5f 100644 --- a/awscli/examples/omics/update-variant-store.rst +++ b/awscli/examples/omics/update-variant-store.rst @@ -20,4 +20,4 @@ Output:: "updateTime": "2022-12-05T18:23:37.686402Z" } -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*. diff --git a/awscli/examples/omics/wait.rst b/awscli/examples/omics/wait.rst index 97821b410506..09125a15e344 100644 --- a/awscli/examples/omics/wait.rst +++ b/awscli/examples/omics/wait.rst @@ -5,4 +5,4 @@ The following ``wait`` example waits for an annotation store's status to be ``AC aws omics wait annotation-store-created \ --name my_ann_store -For more information, see `Omics Analytics `__ in the *Amazon Omics Developer Guide*. +For more information, see `HealthOmics Analytics `__ in the *AWS HealthOmics User Guide*.