common-workflow-language / common-workflow-language/cwltool

import directives not followed in input job objects if cwl:tool is used

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bug help wanted
Dominant language
Python
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Description

Example: https://github.com/common-workflow-language/common-workflow-language/blob/master/site/cwlsite-job.yaml

```
git clone git@github.com:common-workflow-language/common-workflow-language.git
cd common-workflow-language
cwltool site/cwlsite-job.yaml # fails
cwltool site/cwlsite.cwl site/cwlsite-job.yaml # works
```

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