AWS omics documentation change
Summary
Added documentation for Nextflow v26.04 release notes including supported features, deprecations, and HealthOmics compatibility notes
Security assessment
The changes document version-specific feature support and deprecations without addressing vulnerabilities. The isolated network note clarifies existing security boundaries but doesn't introduce new security content.
Diff
diff --git a/omics/latest/dev/workflow-definition-nextflow.md b/omics/latest/dev/workflow-definition-nextflow.md index 2f94bfe59..6988dd166 100644 --- a//omics/latest/dev/workflow-definition-nextflow.md +++ b//omics/latest/dev/workflow-definition-nextflow.md @@ -7 +7 @@ -Use nf-schema and nf-validation pluginsSpecify storage URIsNextflow directivesUse Nextflow profilesExport workflow-level contentExport task contentSpecify the Nextflow syntax version +Use nf-schema and nf-validation pluginsSpecify storage URIsNextflow directivesUse Nextflow profilesExport workflow-level contentExport task contentSpecify the Nextflow syntax versionNextflow v26.04 release notes @@ -30,0 +31,2 @@ Nextflow DSL2 is based on the Groovy programming language, so parameters are dyn + * Nextflow v26.04 release notes + @@ -438,0 +441,25 @@ For Nextflow v25.10.0 and earlier, HealthOmics does not support the v2 parser. +## Nextflow v26.04 release notes + +The following tables summarize HealthOmics support for new features, enhancements, and deprecations released in Nextflow version 26.04. + +### New features and enhancements + +Feature | From version | HealthOmics support | Notes +---|---|---|--- +Strict syntax parser (default) | 26.04 | Yes | Enabled by default from v26.04. Legacy parser available via `syntaxVersion: "v1"` in engine settings. +Record types | 26.04 | Yes | For more information, see [Records](https://docs.seqera.io/nextflow/script#records) in the Seqera Nextflow documentation. +Workflow output summaries | 26.04 | Yes | Prints a summary of workflow outputs on run completion. Output format configurable via `outputFormat` in engine settings. For more information, see [Specify engine settings](./starting-a-run.html#start-run-api-engine-settings). +Agent logging mode | 26.04 | Yes | Configurable via `agentMode` in engine settings. For more information, see [Specify engine settings](./starting-a-run.html#start-run-api-engine-settings). +Module system (Nextflow Registry) | 26.04 | No | HealthOmics workflows run in an isolated network with no outbound internet access. You can include modules directly in your workflow zip. +Static typing (preview) | 26.04 | No | HealthOmics does not support preview features. +Auto-load collection params from files | 26.04 | No | Requires static typing (preview), which HealthOmics does not support. +Multi-revision pipelines checkout | 26.04 | N/A | Not applicable. HealthOmics does not use Git-based pipeline checkout. + +### Deprecations + +Deprecated item | From version | Impact | Recommended action +---|---|---|--- +`listFiles()` method | 26.04 | Deprecation warning | Replace with `listDirectory()`. +`nextflow.enable.strict` flag | 26.04 | No longer needed | Remove from config. Strict mode is now the default. +`manifest.defaultBranch` | 26.04 | No longer needed | Remove from config. HealthOmics does not use Git-based pipeline checkout and has never supported this option. +