AWS omics documentation change

Service: omics · 2026-04-10 · Documentation low

File: omics/latest/dev/workflow-definition-nextflow.md

Summary

Added documentation for Nextflow v25.10 features including export of workflow-level content via /mnt/workflow/output/, support for nf-prov plugin, and alternative task export methods using workflow outputs.

Security assessment

The changes are feature additions and documentation updates for Nextflow workflow capabilities in AWS HealthOmics. There is no mention of security vulnerabilities, security patches, or security features. The updates are purely functional enhancements for data export and workflow management.

Diff

diff --git a/omics/latest/dev/workflow-definition-nextflow.md b/omics/latest/dev/workflow-definition-nextflow.md
index 1d4c39d57..523166e23 100644
--- a//omics/latest/dev/workflow-definition-nextflow.md
+++ b//omics/latest/dev/workflow-definition-nextflow.md
@@ -5 +5 @@
-Use nf-schema and nf-validation pluginsSpecify storage URIsNextflow directivesExport task content
+Use nf-schema and nf-validation pluginsSpecify storage URIsNextflow directivesExport workflow-level contentExport task content
@@ -20,0 +21,2 @@ Nextflow DSL2 is based on the Groovy programming language, so parameters are dyn
+  * Export workflow-level content
+
@@ -38 +40 @@ Summary of HealthOmics support for plugins:
-  * v25.10 – supports `nf-schema`, `nf-core-utils`, and `nf-fgbio`
+  * v25.10 – supports `nf-schema`, `nf-core-utils`, `nf-fgbio`, and `nf-prov`
@@ -248,0 +251,22 @@ The following example shows how to specify task-specific time directives in the
+## Export workflow-level content
+
+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.
+
+The following example shows how to configure the `nf-prov` plugin to write a provenance report to `/mnt/workflow/output/`.
+    
+    
+    prov {
+        formats {
+            bco {
+                file = "/mnt/workflow/output/pipeline_info/manifest.bco.json"
+            }
+        }
+    }
+
+You can also pass this path as a parameter in your run's input JSON. This approach is common with nf-core workflows that use `params.outdir`.
+    
+    
+    {
+        "outdir": "/mnt/workflow/output/"
+    }
+
@@ -309,0 +334,32 @@ 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.
+    
+    
+    process myTask {
+        input:
+        val data
+    
+        output:
+        path 'result.txt'
+    
+        script:
+        """
+        echo ${data} > result.txt
+        """
+    }
+    
+    workflow {
+        main:
+        output_file = myTask('hello')
+    
+        publish:
+        results = output_file
+    }
+    
+    output {
+        results {
+            path '.'
+        }
+    }
+
+For more information about workflow outputs, see [Workflow outputs](https://www.nextflow.io/docs/latest/workflow.html#workflow-output-def) in the Nextflow documentation.
+