tweaks to `examples` set-up to avoid errors

qiime2 / q2cwl

Prototype interface for automatically generating CWL tools from QIIME 2 actions

BSD 3-Clause "New" or "Revised" License

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Closed AmandaBirmingham closed 8 months ago

AmandaBirmingham commented 1 year ago

add --preserve-entire-environment flag to cwltool calls in Makefile to avoid env variable-related error
modify path to input_data in examples/importing-dir/job.yaml to match location of output from examples/exporting-dir.
- exporting-dir is run before importing-dir in the Makefile, and seems to be the intended source of the contents for importing-dir ... at least, I can't find any other :)

Oddant1 commented 9 months ago

Hello @AmandaBirmingham, sorry this was on the back-burner for a while, is this PR good to go? It makes sense to me.

AmandaBirmingham commented 8 months ago

Yes, good to go as far as I know :)