Update cli.md

Co-authored-by: Jorge Ejarque <[email protected]>
Signed-off-by: Phil Ewels <[email protected]>

Author: ewels

docs/reference/cli.md

@@ -742,7 +742,8 @@ $ nextflow lineage view lid://c914d714877cc5c882c55a5428b510b1#output
 
 :::{warning}
 Only outputs described using the {ref}`workflow-outputs` syntax are captured in lineage records.
-If your pipeline only uses {ref}`publishDir` then an empty list will be returned.
+If your pipeline only uses {ref}`publishDir`, an empty list will be returned.
+However, files published via `publishDir` can be accessed using the Lineage ID in the format `lid://<WORKFLOW_LID>/<RELATIVE_PATH>`, where `<RELATIVE_PATH>` is the file's path relative to the workflow's output directory. If the `publishDir` path is not a subpath of the workflow output directory, lineage metadata entries will not be created and a warning message will be displayed.
 :::
 
 Find all lineage records that match a set of key-value pairs: