AWS omics documentation change
Summary
Added new 'Specify engine settings' section documenting how to pass engineSettings map in StartRun requests to control Nextflow behavior without modifying workflows
Security assessment
The change documents new configuration options for Nextflow engine versions and settings, but contains no references to security vulnerabilities, patches, or security-specific features. It focuses on operational controls like version pinning and output formats without addressing authentication, encryption, or access control.
Diff
diff --git a/omics/latest/dev/starting-a-run.md b/omics/latest/dev/starting-a-run.md index f32809149..783d042a1 100644 --- a//omics/latest/dev/starting-a-run.md +++ b//omics/latest/dev/starting-a-run.md @@ -7 +7 @@ -HealthOmics run parametersStarting a run using the consoleStarting a run using the APIGet information about a runVPC networking +HealthOmics run parametersStarting a run using the consoleStarting a run using the APIGet information about a runSpecify engine settingsVPC networking @@ -36,0 +37,2 @@ You specify an IAM service role when you start a run. Optionally, the console ca + * Specify engine settings + @@ -282,0 +285,45 @@ Run metadata isn't deleted if it's not present in the CloudWatch logs. +## Specify engine settings + +For Nextflow v26.04.0 (and selected keys on earlier versions), you can pass an `engineSettings` map in the **StartRun** request to control engine behavior without modifying your workflow. + +The following table describes the supported keys: + +Key | Values | Behavior | Version support +---|---|---|--- +`engineVersion` | `"22.04.0"`, `"23.10.0"`, `"24.10.8"`, `"25.10.0"`, `"26.04.0"` | Pins the Nextflow version for the run. Overrides the version detected from `nextflow.config`. | All Nextflow versions +`syntaxVersion` | `"v1"`, `"v2"` | Selects the syntax parser. For more information, see [Specify the Nextflow syntax version](./workflow-definition-nextflow.html#nextflow-syntax-version). | Nextflow v26.04.0 and later. For v25.10.0 and earlier, only `"v1"` is supported. +`outputFormat` | `"json"`, `"text"`, `"none"` | Sets the format of the engine's stdout/stderr summary. | Nextflow v26.04.0 and later (silently ignored on earlier versions) +`agentMode` | `"true"`, `"false"` (case-insensitive), `"0"`, `"1"`, `0`, `1` | Controls Nextflow agent mode. | Nextflow v26.04.0 and later (silently ignored on earlier versions) +`profile` | Comma-separated profile names | Activates one or more Nextflow configuration profiles. For more information, see [Use Nextflow profiles](./workflow-definition-nextflow.html#nextflow-profiles). | All Nextflow versions + +The following example uses `engineSettings` to pin the Nextflow version and select the legacy syntax parser: + + + { + "engineSettings": { + "engineVersion": "26.04.0", + "syntaxVersion": "v1", + "outputFormat": "json" + } + } + +The following example starts a run with a single Nextflow profile: + + + aws omics start-run \ + --workflow-id workflow-id \ + --role-arn role-arn \ + --output-uri s3://bucket-name/prefix/ \ + --engine-settings '{"profile": "test"}' + +To specify multiple profiles, provide a comma-separated list as shown in the example below. Nextflow applies profiles in the order they are specified in the command line. If multiple profiles define the same setting, later profiles override earlier ones. In the example below, `test` is applied first and then `docker`, so any conflicting settings in `docker` take precedence over `test`. + + + aws omics start-run \ + --workflow-id workflow-id \ + --role-arn role-arn \ + --output-uri s3://bucket-name/prefix/ \ + --engine-settings '{"profile": "test,docker"}' + +The `engineSettings` field is returned in the **GetRun** response, showing which engine settings were applied to the run. +