Question: change temp folder in cwl
1
gravatar for roalva1
20 months ago by
roalva180
Spain
roalva180 wrote:

Hello,

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

Thanks

cwl commonworkflowlanguage • 824 views
ADD COMMENTlink modified 19 months ago by stian30 • written 20 months ago by roalva180

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

ADD REPLYlink written 19 months ago by Michael R. Crusoe1.8k
3
gravatar for stian
19 months ago by
stian30
stian30 wrote:

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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by stian30
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