Move Intermediate files

CWL Questions
1

I am trying to create a workflow comprised of several steps; 1 tool per step. Whenever I run the whole workflow, the intermediate files are getting deleted. And I can not access them anymore. But I would like to save those intermediate files in another directory.

Is there any way to keep the intermediate files generated by workflow at a certain place? like a specific directory?

Thanks in advance!

2

Welcome @HrishiDhondge

It depends on your CWL runner. With the reference CWL runner (cwltool) you can use the --cachedir option to specify a place to store intermediate results. Bonus: it will speed up re-runs when you are running the equivalent same step again.

I hope that helps.

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