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157 changes: 153 additions & 4 deletions docs/reference/cli.md
Original file line number Diff line number Diff line change
Expand Up @@ -1011,6 +1011,133 @@ The `log` command is used to query the execution metadata associated with pipeli

`-f, -fields`
: Comma-separated list of fields to include in the printed log. Use the `-l` option to see the list of available fields.
: 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`.

`-F, -filter`
: Filter log entries by a custom expression, e.g. `process =~ /hello.*/ && status == 'COMPLETED'`.
Expand Down Expand Up @@ -1344,10 +1471,32 @@ The `run` command is used to execute a local pipeline script or remote pipeline
: Use the specified Conda environment package or file (must end with `.yml` or `.yaml`)

`-with-dag` (`dag-<timestamp>.html`)
: Create pipeline DAG file.
: :::{versionchanged} 23.10.0
The default format was changed from `dot` to `html`.
:::
: Create pipeline DAG file. Default format: `html`.
: Supported file formats:

`dot`
: Graphviz [DOT](http://www.graphviz.org/content/dot-language) file.

`gexf`
: Graph Exchange XML file (Gephi).

`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.

`-with-docker`
: Enable process execution in a Docker container.
Expand Down
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