From ec7b5ca5a7c86897e6c781474908ae594ff56b31 Mon Sep 17 00:00:00 2001 From: Marcel Loose Date: Thu, 14 Nov 2024 11:27:02 +0100 Subject: [PATCH] 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. --- docs/running/cliOptions.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/running/cliOptions.rst b/docs/running/cliOptions.rst index 58e204d916..00ef42aa7d 100644 --- 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-`` 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