AWS omics documentation change
Summary
Added documentation for Nextflow profiles and syntax version specification. Updated plugin support for v26.04, expanded export functionality coverage to later versions, and added guidance on legacy syntax compatibility.
Security assessment
Changes focus on feature enhancements (profiles, syntax versioning) and compatibility updates. No security vulnerabilities, patches, or security-specific configurations are mentioned. Updates to export paths and plugin versions lack security context.
Diff
diff --git a/omics/latest/dev/workflow-definition-nextflow.md b/omics/latest/dev/workflow-definition-nextflow.md index df8a42a0b..2f94bfe59 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 directivesExport workflow-level contentExport task content +Use nf-schema and nf-validation pluginsSpecify storage URIsNextflow directivesUse Nextflow profilesExport workflow-level contentExport task contentSpecify the Nextflow syntax version @@ -22,0 +23,2 @@ Nextflow DSL2 is based on the Groovy programming language, so parameters are dyn + * Use Nextflow profiles + @@ -26,0 +29,2 @@ Nextflow DSL2 is based on the Groovy programming language, so parameters are dyn + * Specify the Nextflow syntax version + @@ -42 +46 @@ Summary of HealthOmics support for plugins: - * v25.10 – supports `nf-schema`, `nf-core-utils`, `nf-fgbio`, and `nf-prov` + * v25.10, v26.04 – supports `nf-schema`, `nf-core-utils`, `nf-fgbio`, and `nf-prov` @@ -54,0 +59,2 @@ HealthOmics provides the following support for Nextflow plugins: + * For Nextflow v26.04, HealthOmics pre-installs the [email protected], [email protected], [email protected], and [email protected] plugins. + @@ -254,0 +261,48 @@ The following example shows how to specify task-specific time directives in the +## Use Nextflow profiles + +Nextflow profiles are named sets of configuration settings that you can select at runtime. Define profiles in the `profiles` block of your `nextflow.config` file: + + + profiles { + standard { + process.cpus = 2 + process.memory = '4 GB' + } + + production { + process.cpus = 16 + process.memory = '64 GB' + params.input = 's3://bucket/production-data.bam' + } + } + +When you start a run, specify one or more profiles using the `engineSettings` parameter. HealthOmics passes the `-profile` flag to the Nextflow engine. For more information, see [Specify engine settings](./starting-a-run.html#start-run-api-engine-settings). + + + aws omics start-run \ + --workflow-id workflow-id \ + --role-arn role-arn \ + --output-uri s3://bucket/prefix/ \ + --engine-settings '{"profile": "production"}' + +When multiple profiles are specified (for example, `"test,docker"`), Nextflow applies them in the order they are specified in the command line. Later profiles override earlier ones for conflicting settings. For Nextflow versions lower than 26, profiles are applied in the order they are defined in the configuration file instead of command line order. + +Note the following: + + * Profile support is available for all HealthOmics supported Nextflow versions. + + * Profiles can contain parameters, process directives, `includeConfig` statements, and manifest overrides (including `manifest.nextflowVersion`). + + * Explicit run parameters take precedence over profile-defined parameter values. + + * If you specify a nonexistent profile, HealthOmics returns a validation error. + + * Profiles must be defined in the workflow definition zip file. HealthOmics doesn't support fetching profile definitions from external sources. + + * If you don't specify a profile, the run uses the `standard` profile if it's defined under profiles in the workflow definition. Otherwise, the run uses the default (top-level) configuration. + + * When using profiles, we recommend pinning the Nextflow version in your workflow definition using `manifest.nextflowVersion` to ensure consistent profile application behavior across runs. + + + + @@ -257 +311 @@ The following example shows how to specify task-specific time directives in the -For Nextflow v25.10, you can export files produced outside of individual tasks, such as provenance reports or pipeline DAGs. To export these files, write them to `/mnt/workflow/output/`. HealthOmics exports files placed in this directory to the `output/` prefix in your run's Amazon S3 output location. +For Nextflow v25.10 and later, you can export files produced outside of individual tasks, such as provenance reports or pipeline DAGs. To export these files, write them to `/mnt/workflow/output/`. HealthOmics exports files placed in this directory to the `output/` prefix in your run's Amazon S3 output location. @@ -338 +392 @@ For workflows written in Nextflow, define a **publishDir** directive to export t -For Nextflow v25.10, as an alternative to `publishDir`, you can use workflow outputs to export task content. The following example shows how to define a workflow `output` block that exports task results to Amazon S3. +For Nextflow v25.10 and later, as an alternative to `publishDir`, you can use workflow outputs to export task content. The following example shows how to define a workflow `output` block that exports task results to Amazon S3. @@ -369,0 +424,15 @@ For more information about workflow outputs, see [Workflow outputs](https://www. +## Specify the Nextflow syntax version + +Nextflow v26.04.0 uses the strict (v2) syntax parser by default. This is a breaking change for workflows written using the legacy (v1) syntax, which is the default in Nextflow v25.10.0 and earlier. For information about the v2 syntax, see [Strict syntax](https://docs.seqera.io/nextflow/strict-syntax) in the Seqera Nextflow documentation. + +To run a workflow authored against the legacy (v1) parser, set `engineSettings.syntaxVersion` to `v1` in the **StartRun** request: + + + { + "engineSettings": { + "syntaxVersion": "v1" + } + } + +For Nextflow v25.10.0 and earlier, HealthOmics does not support the v2 parser. +