AWS omics documentation change

Service: omics · 2026-07-04 · Documentation low

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

Summary

Added documentation for generating Nextflow execution reports (report, timeline, trace, dag) and exporting them to S3 output location. Specified requirements for task containers to include 'ps' command and limitations for workflow diagram formats.

Security assessment

The change documents operational reporting features without addressing vulnerabilities or security weaknesses. It focuses on workflow output configuration and container requirements for metrics collection, with no evidence of security fixes or security-specific content.

Diff

diff --git a/omics/latest/dev/workflow-definition-nextflow.md b/omics/latest/dev/workflow-definition-nextflow.md
index b94affed7..51931777c 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 versionUsing scratch storage efficiently in NextflowNextflow v26.04 release notes
+Use nf-schema and nf-validation pluginsSpecify storage URIsNextflow directivesUse Nextflow profilesExport workflow-level contentExport task contentGenerate Nextflow execution reportsSpecify the Nextflow syntax versionUsing scratch storage efficiently in NextflowNextflow v26.04 release notes
@@ -28,0 +29,2 @@ Nextflow DSL2 is based on the Groovy programming language, so parameters are dyn
+  * Generate Nextflow execution reports
+
@@ -427,0 +430,39 @@ For more information about workflow outputs, see [Workflow outputs](https://www.
+## Generate Nextflow execution reports
+
+Nextflow can produce four built-in reports for each run: an execution report (`report`), a timeline (`timeline`), a trace file (`trace`), and a workflow diagram (`dag`). For HealthOmics to export these files to your run's Amazon S3 output location, configure each one to write its output under `/mnt/workflow/output/` in your `nextflow.config` file:
+    
+    
+    report {
+        enabled = true
+        file = '/mnt/workflow/output/report.html'
+        overwrite = true
+    }
+    
+    timeline {
+        enabled = true
+        file = '/mnt/workflow/output/timeline.html'
+        overwrite = true
+    }
+    
+    trace {
+        enabled = true
+        file = '/mnt/workflow/output/trace.txt'
+        overwrite = true
+    }
+    
+    dag {
+        enabled = true
+        file = '/mnt/workflow/output/dag.html'
+        overwrite = true
+    }
+
+HealthOmics exports files written under `/mnt/workflow/output/` to the `output/` prefix in your run's Amazon S3 output location. For more information about this export path, see Export workflow-level content. Reports written outside `/mnt/workflow/output/` are not exported to your run's Amazon S3 output location.
+
+###### Task containers must include ps
+
+When the `report`, `timeline`, or `trace` report is enabled, Nextflow collects per-task metrics by invoking `ps` inside each task container. The container image that you specify with the `container` directive must include the `ps` command. On most Linux distributions, install it with the `procps` (Debian/Ubuntu) or `procps-ng` (Amazon Linux, Red Hat, Fedora) package. If a process does not declare a `container` directive, HealthOmics runs the task in a default container that already includes `ps`.
+
+###### Workflow diagram format
+
+The `dag` report supports several output formats, selected by the extension of `dag.file`. The HTML, Mermaid, and DOT formats are rendered directly by Nextflow and do not require additional tooling. The PDF, PNG, and SVG formats require Graphviz, which is not included in HealthOmics's Nextflow engine. If `dag.file` is set to a PDF, PNG, or SVG path, Nextflow logs a warning and writes the workflow diagram as a `.dot` source file in its place; the run still completes successfully. We recommend setting `dag.file` to a `.html`, `.mmd`, or `.dot` path to avoid the warning and produce the requested format.
+