It seems that actions in the generated workflows do not preserve the order of the input artefacts of the corresponding tools. This leads to issues for us, because we rely on input labels for parsing CCT expressions.
This is a limitation of APE that I can possibly hack around somewhat by re-matching it to the tools, but it's unsatisfying because this only works if no tools have the same input types.
It seems that actions in the generated workflows do not preserve the order of the input artefacts of the corresponding tools. This leads to issues for us, because we rely on input labels for parsing CCT expressions.
This is a limitation of APE that I can possibly hack around somewhat by re-matching it to the tools, but it's unsatisfying because this only works if no tools have the same input types.