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Let inline bash scripts exit on error

Marcel Loose requested to merge bash-exit-on-error into master

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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