change temp folder in cwl

Question

[roalva1]

Hello,

is there any way I can change temp folder to a class Workflow cwl file? or inside a CommandLineTool class?

Thanks

[Michael R. Crusoe]

Hello roalva1, thank you for your question. Can you provide more information or context?

Answer 1

[stian]

Different CWL implementations use temporary folders differently.

If you use the reference implementation cwltool you can use --tmpdir-prefix and --tmp-outdir-prefix to change where all temporary files are stored, for instance:

cwl-runner --tmp-outdir-prefix=/mnt/large/tmp1 --tmpdir-prefix=/mnt/large/tmp1 wc-tool.cwl wc-job.json

It is not possible in cwltool to set the temporary directory per step, per workflow or per job.

Other engines might have different ways of setting the temporary storage. For instance Toil uses instead the TOIL_WORKDIR environment variable or the --workDir parameter.