diff --git a/docs/usage.md b/docs/usage.md index 55ade60..a917237 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -64,6 +64,12 @@ optional arguments: every command being run by CABINET to stdout. Otherwise CABINET will only print warnings, errors, and minimal output. + -w, --work-dir Valid absolute path where intermediate results (prebibsnet + through postbibsnet stage outputs) should be stored. By + default, this outputs to /tmp/cabinet. This directory is + is deleted at the end of postbibsnet after results are + copied into the "bibsnet" derivatives directory. + Example: /path/to/working/directory -z, --brain-z-size Include this flag to infer participants' brain height (z) using the participants.tsv brain_z_size column. Otherwise, CABINET will estimate the brain height from