Improve documentation of workDir option

Improved the documentation of the `--workDir` option, by adding an explanation that the `--tmp-outdir-prefix` will be used for CWL workflows.
DataBiosphere · Nov 14, 2024 · f71ddf3 · f71ddf3
1 parent a373ff1
commit f71ddf3
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/docs/running/cliOptions.rst b/docs/running/cliOptions.rst
@@ -89,8 +89,10 @@ about the performance of jobs.
                         directory. Temp files and folders will be placed in a
                         directory ``toil-<workflowID>`` within workDir. The
                         workflowID is generated by Toil and will be reported in
-                        the workflow logs. Default is the temporary output
-                        directory (see ``--tmp-outdir-prefix``). This
+                        the workflow logs. Default is determined by the
+                        variables (TMPDIR, TEMP, TMP) via mkdtemp. For CWL
+                        workflows, the temporary output directory is used
+                        (see CWL option ``--tmp-outdir-prefix``). This
                         directory needs to exist on all machines running jobs;
                         if capturing standard output and error from batch
                         system jobs is desired, it will generally need to be on