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CWL v1.2 is more explicit about the way that strings in embedded code that contain a dollar sign ($) must be escaped. See https://www.commonwl.org/v1.2/Workflow.html#String_interpolation. It turned out that a few workflow steps contained inline Bash code with improperly escaped variables references. This has been fixed.


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Most of the inline bash scripts in the CWL files *ignore* errors, which is undesirable. This fix adds a `set -e` to all the inline scripts that did not have one yet. Note that adding a `-e` to the `#!/bin/bash` does *not* work, because the script is not invoked as an executable but as `bash <script-file>`.


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