A brief documentation of the pipeline rules is given in 'pipeline_documentation.md'.
ATTENTION: Descriptions of tools are copy-pasted from their respective homepages, so this documentation cannot be used in a publication.
Everyone has to check the sections on the rules they have added, as I merely tried to understand what has been done, without feedback from the rule authors. This applies especially to @katsanto, also check the input samples table description (!!!), and to @devagy74 I guess. Work by @burri0000 and @bakma had not been included at the time of writing, so the respective sections have to be added to the documentation by these guys.
I did not add the documentation to the README because I didn't want to step on anyone's toes.
This closes #60 (closed) and #57 (closed) .