Skip to content

Instantly share code, notes, and snippets.

@ionox0

ionox0/toil_tmp_dirs.md

Last active December 11, 2019 17:15
Show Gist options
  • Save ionox0/225240e0952f2c8c363bd0e74a941936 to your computer and use it in GitHub Desktop.
Save ionox0/225240e0952f2c8c363bd0e74a941936 to your computer and use it in GitHub Desktop.
Download ZIP
Understanding Toil temporary directories
Raw
toil_tmp_dirs.md

Here are all of the current arguments related to input / output / temporary directories used by Toil and cwltool:

cwltool:

--outdir - Final outputs directory

--tmpdir-prefix - This is a prefix for folders that do not yet exist, but will be used as intermediate working directories

--tmp-outdir-prefix - This is a prefix for folders that do not yet exist, but will be used as intermediate output directories

toil-cwl-runner:

--workDir - This is the folder in which there will be created subfolders that will be set as the working directories for all tools running in the workflow (defaults to TMPDIR if not set)

(I assume this overrides the cwltool --tmpdir-prefix and --tmp-outdir-prefix, but I'm not sure)

--outDir - This is the folder that the final outputs of the workflow will be copied to once it is completed

(I assume this overrides the cwltool --outdir)

--jobstore - This is the folder where all state tracking information for the jobs in the workflow is kept, including stats records

Why are these options for toil-cwl-runner?

--tmp-outdir-prefix - ??

--tmpdir-prefix - ??

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment