Add workflow.report config scopes [e2e prod]

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

docs/reference/cli.md

@@ -1748,7 +1748,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
   $ nextflow run main.nf -profile docker
   ```
 
-- Execute a pipeline and generate the summary HTML report. For more information on the metrics, please refer the {ref}`tracing-page` section:
+- Execute a pipeline and generate the summary HTML report. For more information on the metrics, please refer the {ref}`reports-page` section:
 
   ```console
   $ nextflow run main.nf -with-report

docs/reference/config.md

@@ -552,6 +552,10 @@ The following settings are available:
 
 ## `dag`
 
+:::{deprecated} 26.04.0
+Use the `workflow.report.dag` scope instead.
+:::
+
 The `dag` scope controls the generation of the {ref}`workflow-diagram`.
 
 The following settings are available:
@@ -1350,6 +1354,10 @@ The following settings are available:
 
 ## `report`
 
+:::{deprecated} 26.04.0
+Use the `workflow.report.execution` scope instead.
+:::
+
 The `report` scope controls the generation of the {ref}`execution-report`.
 
 The following settings are available:
@@ -1570,6 +1578,10 @@ The following settings are available:
 
 ## `timeline`
 
+:::{deprecated} 26.04.0
+Use the `workflow.report.timeline` scope instead.
+:::
+
 The `timeline` scope controls the generation of the {ref}`timeline-report`.
 
 The following settings are available:
@@ -1622,6 +1634,10 @@ The following settings are available:
 
 ## `trace`
 
+:::{deprecated} 26.04.0
+Use the `workflow.report.trace` scope instead.
+:::
+
 The `trace` scope controls the generation of the {ref}`trace-report`.
 
 The following settings are available:
@@ -1905,9 +1921,6 @@ The following settings are available:
 
 ## `workflow`
 
-:::{versionadded} 24.10.0
-:::
-
 The `workflow` scope provides workflow execution options.
 
 The following settings are available:
@@ -1918,11 +1931,26 @@ The following settings are available:
 : When `true`, the pipeline will exit with a non-zero exit code if any failed tasks are ignored using the `ignore` {ref}`error strategy <process-error-strategy>` (default: `false`).
 
 `workflow.onComplete`
+: :::{deprecated} 25.10.0
+  Use a {ref}`trace observer <plugins-trace-observers>` in a plugin to add custom workflow handlers to a pipeline via configuration.
+  :::
 : Specify a closure that will be invoked at the end of a workflow run (including failed runs). See {ref}`workflow-handlers` for more information.
 
 `workflow.onError`
+: :::{deprecated} 25.10.0
+  Use a {ref}`trace observer <plugins-trace-observers>` in a plugin to add custom workflow handlers to a pipeline via configuration.
+  :::
 : Specify a closure that will be invoked if a workflow run is terminated. See {ref}`workflow-handlers` for more information.
 
+### `workflow.output`
+
+:::{versionadded} 24.10.0
+:::
+
+The `workflow.output` scope controls how workflow outputs are published.
+
+The following settings are available:
+
 `workflow.output.contentType`
 : *Currently only supported for S3.*
 : Specify the media type, also known as [MIME type](https://developer.mozilla.org/en-US/docs/Web/HTTP/MIME_types), of published files (default: `false`). Can be a string (e.g. `'text/html'`), or `true` to infer the content type from the file extension.
@@ -1995,3 +2023,79 @@ The following settings are available:
   ```groovy
   workflow.output.tags = [FOO: 'hello', BAR: 'world']
   ```
+
+### `workflow.report`
+
+:::{versionadded} 26.04.0
+:::
+
+The `workflow.report` scope controls the standard {ref}`reports <reports-page>` provided by Nextflow.
+
+The following settings are available:
+
+**`workflow.report.dag`**
+
+`workflow.report.dag.depth`
+: *Supported by the HTML and Mermaid renderers.*
+: Controls the maximum depth at which to render sub-workflows (default: no limit).
+
+`workflow.report.dag.direction`
+: *Supported by the Graphviz, DOT, HTML and Mermaid renderers.*
+: Controls the direction of the DAG, can be `'LR'` (left-to-right) or `'TB'` (top-to-bottom) (default: `'TB'`).
+
+`workflow.report.dag.enabled`
+: Create the {ref}`workflow-diagram` on workflow completion (default: `false`).
+
+`workflow.report.dag.file`
+: DAG file path relative to the output directory (default: `'dag-<timestamp>.html'`).
+: The output format is inferred from the file extension. See {ref}`config-dag` for the list of supported formats.
+
+`workflow.report.dag.overwrite`
+: When `true` overwrites any existing DAG file with the same name (default: `false`).
+
+`workflow.report.dag.verbose`
+: *Only supported by the HTML and Mermaid renderers.*
+: When `false`, channel names are omitted, operators are collapsed, and empty workflow inputs are removed (default: `false`).
+
+**`workflow.report.execution`**
+
+`workflow.report.execution.enabled`
+: Create the {ref}`execution-report` on workflow completion (default: `false`).
+
+`workflow.report.execution.file`
+: Report file path relative to the output directory (default: `'report-<timestamp>.html'`).
+
+`workflow.report.execution.overwrite`
+: Overwrite any existing report file with the same name (default: `false`).
+
+**`workflow.report.timeline`**
+
+`workflow.report.timeline.enabled`
+: Create the {ref}`timeline-report` on workflow completion (default: `false`).
+
+`workflow.report.timeline.file`
+: Timeline file path relative to the output directory (default: `'timeline-<timestamp>.html'`).
+
+`workflow.report.timeline.overwrite`
+: Overwrite any existing timeline file with the same name (default: `false`).
+
+**`workflow.report.trace`**
+
+`workflow.report.trace.enabled`
+: Create the {ref}`trace-report` on workflow completion (default: `false`).
+
+`workflow.report.trace.fields`
+: Comma-separated list of fields to include in the trace file.
+: See {ref}`config-trace` for the list of available fields.
+
+`workflow.report.trace.file`
+: Trace file path relative to the output directory (default: `'trace-<timestamp>.txt'`).
+
+`workflow.report.trace.overwrite`
+: Overwrite any existing trace file with the same name (default: `false`).
+
+`workflow.report.trace.raw`
+: Report trace metrics as raw numbers where applicable, i.e. report duration values in milliseconds and memory values in bytes (default: `false`).
+
+`workflow.report.trace.sep`
+: Character used to separate values in each row (default: `\t`).

docs/reports.md

@@ -1,4 +1,4 @@
-(tracing-page)=
+(reports-page)=
 
 # Reports
 
@@ -121,6 +121,24 @@ report {
 
 See {ref}`config-report` for the list of available config options.
 
+:::{versionadded} 26.04.0
+:::
+
+Use the `workflow.report.execution` scope instead:
+
+```groovy
+workflow {
+    report {
+        execution {
+            enabled = true
+            file = 'report.html'
+        }
+    }
+}
+```
+
+It will automatically create the execution report in the pipeline output directory instead of the launch directory.
+
 ### Summary
 
 The **Summary** section reports the execution status, the launch command, overall execution time, and other workflow metadata:
@@ -185,6 +203,24 @@ timeline {
 
 See {ref}`config-timeline` for the list of available config options.
 
+:::{versionadded} 26.04.0
+:::
+
+Use the `workflow.report.timeline` scope instead:
+
+```groovy
+workflow {
+    report {
+        timeline {
+            enabled = true
+            file = 'timeline.html'
+        }
+    }
+}
+```
+
+It will automatically create the timeline report in the pipeline output directory instead of the launch directory.
+
 (trace-report)=
 
 ## Trace file
@@ -231,6 +267,24 @@ trace {
 
 See {ref}`config-trace` for the list of available config options.
 
+:::{versionadded} 26.04.0
+:::
+
+Use the `workflow.report.trace` scope instead:
+
+```groovy
+workflow {
+    report {
+        trace {
+            enabled = true
+            file = 'trace.txt'
+        }
+    }
+}
+```
+
+It will automatically create the trace report in the pipeline output directory instead of the launch directory.
+
 (workflow-diagram)=
 
 ## Workflow diagram
@@ -259,3 +313,21 @@ nextflow run rnaseq-nf -preview -with-dag
 ```
 
 See {ref}`config-dag` for the list of available config options.
+
+:::{versionadded} 26.04.0
+:::
+
+Use the `workflow.report.dag` scope instead:
+
+```groovy
+workflow {
+    report {
+        dag {
+            enabled = true
+            file = 'dag.html'
+        }
+    }
+}
+```
+
+It will automatically create the DAG report in the pipeline output directory instead of the launch directory.

modules/nextflow/src/main/groovy/nextflow/config/WorkflowConfig.groovy

@@ -20,6 +20,10 @@ import nextflow.config.spec.ConfigOption
 import nextflow.config.spec.ConfigScope
 import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
+import nextflow.trace.config.DagConfig
+import nextflow.trace.config.ReportConfig
+import nextflow.trace.config.TimelineConfig
+import nextflow.trace.config.TraceConfig
 
 @ScopeName("workflow")
 @Description("""
@@ -34,25 +38,34 @@ class WorkflowConfig implements ConfigScope {
     """)
     final boolean failOnIgnore
 
+    @Deprecated
     @ConfigOption
     @Description("""
         Specify a closure that will be invoked at the end of a workflow run (including failed runs).
     """)
     final Closure onComplete
 
+    @Deprecated
     @ConfigOption
     @Description("""
         Specify a closure that will be invoked if a workflow run is terminated.
     """)
     final Closure onError
 
     @Description("""
-        The `workflow.output` scope provides options for publishing workflow outputs.
-
+        The `workflow.output` scope controls how workflow outputs are published.
+    
         [Read more](https://nextflow.io/docs/latest/reference/config.html#workflow)
     """)
     final WorkflowOutputConfig output
 
+    @Description("""
+        The `workflow.report` scope controls the standard reports provided by Nextflow.
+    
+        [Read more](https://nextflow.io/docs/latest/reference/config.html#workflow)
+    """)
+    final WorkflowReportConfig report
+
     /* required by extension point -- do not remove */
     WorkflowConfig() {}
 
@@ -61,6 +74,7 @@ class WorkflowConfig implements ConfigScope {
         onComplete = opts.onComplete as Closure
         onError = opts.onError as Closure
         output = new WorkflowOutputConfig(opts.output as Map ?: Collections.emptyMap())
+        report = new WorkflowReportConfig(opts.report as Map ?: Collections.emptyMap())
     }
 
 }
@@ -124,9 +138,6 @@ class WorkflowOutputConfig implements ConfigScope {
     """)
     final Map tags
 
-    /* required by extension point -- do not remove */
-    WorkflowOutputConfig() {}
-
     WorkflowOutputConfig(Map opts) {
         contentType = opts.contentType
         copyAttributes = opts.copyAttributes as boolean
@@ -139,3 +150,23 @@ class WorkflowOutputConfig implements ConfigScope {
     }
 
 }
+
+@CompileStatic
+class WorkflowReportConfig implements ConfigScope {
+
+    final DagConfig dag
+
+    final ReportConfig execution
+
+    final TimelineConfig timeline
+
+    final TraceConfig trace
+
+    WorkflowReportConfig(Map opts) {
+        dag = new DagConfig(opts.dag as Map ?: Collections.emptyMap())
+        execution = new ReportConfig(opts.execution as Map ?: Collections.emptyMap())
+        timeline = new TimelineConfig(opts.timeline as Map ?: Collections.emptyMap())
+        trace = new TraceConfig(opts.trace as Map ?: Collections.emptyMap())
+    }
+
+}