docs: Update reports page (#6645) [ci fast]

Co-authored-by: Ben Sherman <bentshermann@gmail.com>

Author: 2 people

docs/_static/report-resources-min.png

@@ -1020,7 +1020,9 @@ The `log` command is used to query the execution metadata associated with pipeli
 : Show log entries for runs executed *but* the specified one.
 
 `-f, -fields`
-: Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
+: Comma-separated list of fields to include in the printed log.
+: The same fields as the `trace.fields` option can be specified here, as well as `stdout` and `stderr`. The trace fields `%cpu` and `%mem` must be specified as `pcpu` and `pmem`, respectively.
+: Use the `-l` option to see the complete list of available fields.
 
 `-F, -filter`
 : Filter log entries by a custom expression, e.g. `process =~ /hello.*/ && status == 'COMPLETED'`.

docs/_static/report-summary-min.png

@@ -556,7 +556,7 @@ The following settings are available:
 
 ## `dag`
 
-The `dag` scope controls the workflow diagram generated by Nextflow.
+The `dag` scope controls the generation of the {ref}`workflow-diagram`.
 
 The following settings are available:
 
@@ -578,6 +578,32 @@ The following settings are available:
 `dag.file`
 : Graph file name (default: `'dag-<timestamp>.html'`).
 
+: The output format is inferred from the file extension. The following formats are supported:
+
+  `dot`
+  : Graphviz [DOT](http://www.graphviz.org/content/dot-language) file.
+
+  `gexf`
+  : Graph Exchange XML Format ([GEXF](https://gexf.net/)).
+
+  `html`
+  : HTML file with Mermaid diagram.
+
+  `mmd`
+  : Mermaid diagram.
+
+  `pdf`
+  : *Requires [Graphviz](http://www.graphviz.org).*
+  : Graphviz PDF file.
+
+  `png`
+  : *Requires [Graphviz](http://www.graphviz.org)*
+  : Graphviz PNG file.
+
+  `svg`
+  : *Requires [Graphviz](http://www.graphviz.org)*
+  : Graphviz SVG file.
+
 `dag.overwrite`
 : When `true` overwrites any existing DAG file with the same name (default: `false`).
 
@@ -1334,7 +1360,7 @@ The following settings are available:
 
 ## `report`
 
-The `report` scope allows you to configure the workflow {ref}`execution-report`.
+The `report` scope controls the generation of the {ref}`execution-report`.
 
 The following settings are available:
 
@@ -1474,12 +1500,12 @@ The following settings are available:
 
 ## `timeline`
 
-The `timeline` scope controls the execution timeline report generated by Nextflow.
+The `timeline` scope controls the generation of the {ref}`timeline-report`.
 
 The following settings are available:
 
 `timeline.enabled`
-: Create the timeline report on workflow completion file (default: `false`).
+: Create the execution timeline on workflow completion (default: `false`).
 
 `timeline.file`
 : Timeline file name (default: `'timeline-<timestamp>.html'`).
@@ -1516,15 +1542,143 @@ The following settings are available:
 
 ## `trace`
 
-The `trace` scope controls the layout of the execution trace file generated by Nextflow.
+The `trace` scope controls the generation of the {ref}`trace-report`.
 
 The following settings are available:
 
 `trace.enabled`
-: Create the execution trace file on workflow completion (default: `false`).
+: Create the trace file on workflow completion (default: `false`).
 
 `trace.fields`
-: Comma-separated list of {ref}`trace fields <trace-fields>` to include in the report.
+: Comma-separated list of fields to include in the trace file.
+
+: Available fields:
+
+  `task_id`
+  : Task ID.
+
+  `hash`
+  : Task hash code.
+
+  `native_id`
+  : Task ID given by the underlying execution system e.g. POSIX process PID when executed locally, job ID when executed by a grid engine, etc.
+
+  `process`
+  : Nextflow process name.
+
+  `tag`
+  : User provided identifier associated with this task.
+
+  `name`
+  : Task name.
+
+  `status`
+  : Task status. Options: `NEW`, `SUBMITTED`, `RUNNING`, `COMPLETED`, `FAILED`, and `ABORTED`.
+
+  `exit`
+  : POSIX process exit status.
+
+  `module`
+  : Environment module used to run the task.
+
+  `container`
+  : Docker image name used to execute the task.
+
+  `cpus`
+  : The CPUs number request for the task execution.
+
+  `time`
+  : The time request for the task execution
+
+  `disk`
+  : The disk space request for the task execution.
+
+  `memory`
+  : The memory request for the task execution.
+
+  `attempt`
+  : Attempt at which the task completed.
+
+  `submit`
+  : Timestamp when the task has been submitted.
+
+  `start`
+  : Timestamp when the task execution has started.
+
+  `complete`
+  : Timestamp when task execution has completed.
+
+  `duration`
+  : Time elapsed to complete since the submission.
+
+  `realtime`
+  : Task execution time i.e. delta between completion and start timestamp.
+
+  `queue`
+  : The queue that the executor attempted to run the process on.
+
+  `%cpu`
+  : Percentage of CPU used by the process.
+
+  `%mem`
+  : Percentage of memory used by the process.
+
+  `rss`
+  : Real memory (resident set) size of the process. Equivalent to `ps -o rss` .
+
+  `vmem`
+  : Virtual memory size of the process. Equivalent to `ps -o vsize` .
+
+  `peak_rss`
+  : Peak of real memory. Data is read from field `VmHWM` in `/proc/$pid/status` file.
+
+  `peak_vmem`
+  : Peak of virtual memory. Data is read from field `VmPeak` in `/proc/$pid/status` file.
+
+  `rchar`
+  : Number of bytes the process read, using any read-like system call from files, pipes, tty, etc. Data is read from `/proc/$pid/io`.
+
+  `wchar`
+  : Number of bytes the process wrote, using any write-like system call. Data is read from `/proc/$pid/io`.
+
+  `syscr`
+  : Number of read-like system call invocations that the process performed. Data is read from `/proc/$pid/io`.
+
+  `syscw`
+  : Number of write-like system call invocations that the process performed. Data is read from `/proc/$pid/io`.
+
+  `read_bytes`
+  : Number of bytes the process directly read from disk. Data is read from `/proc/$pid/io`.
+
+  `write_bytes`
+  : Number of bytes the process originally dirtied in the page-cache (assuming they will go to disk later). Data is read from `/proc/$pid/io`.
+
+  `vol_ctxt`
+  : Number of voluntary context switches. Data is read from field `voluntary_ctxt_switches` in `/proc/$pid/status` file.
+
+  `inv_ctxt`
+  : Number of involuntary context switches. Data is read from field `nonvoluntary_ctxt_switches` in `/proc/$pid/status` file.
+
+  `env`
+  : The variables defined in task execution environment.
+
+  `workdir`
+  : The directory path where the task was executed.
+
+  `script`
+  : The task command script.
+
+  `scratch`
+  : The value of the process `scratch` directive.
+
+  `error_action`
+  : The action applied on error for task failure.
+
+  `hostname`
+  : The host on which the task was executed. Supported only for the Kubernetes executor yet. Activate with `k8s.fetchNodeName = true` in the Nextflow config file.
+
+  `cpu_model`
+  : The name of the CPU model used to execute the task. This data is read from`/proc/cpuinfo`.
 
 `trace.file`
 : Trace file name (default: `'trace-<timestamp>.txt'`).