Updates to make this pipeline work with the new modular environment as well #13
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I know this branch has been closed in terms of development, but most of the changes proposed here are needed for a more stable behaviour in the new environment whilst removing the need of
ENSCODE. I'm aware there are a few Python-related changes oriented to an improved code readability more than functionality, but they helped me ensure the code was working as expected with the changes.Note: these changes have also been tested with the previous software environment and they work too.