iprotsyuk
commented
6 years ago Hi @jeep3,
- "stub.txt" is just an empty file. Its name is a key-word meaning that no input is provided to a KNIME node. It's definitely a counter-intuitive part of Optimus usage, but unfortunately, KNIME doesn't allow a workflow to run in case any "Input File" node has an empty input. That's why such a placeholder filename is being used.
- groupmapping file contains associations between sample files names and study groups (e.g. treated/untreated or anything else) they belong to. The usage of such a file may be convenient for advanced GNPS users who can generate it with some GNPS tools. However, if you want to specify study groups in Optimus, you can simply put group identifiers (again e.g. "treated" and "untreated") into the 3rd column of the experimental design spreadsheet. Note that using study groups is not obligatory, and you can run Optimus without it. The information about study groups enables advanced filtering of LC-MS features, but, again, it's not crucial. Since you're just getting started with Optimus, I'd suggest just using the stub file for the groupmapping input.
Let me know if anything isn't clear.
jeep3
Hi iprotsyuk I have a question to consult you. when i study the video of GNPS Trinity workflow(https://www.youtube.com/watch?v=zDcY7iuvyQY&t=4s), The Optimus workflow contain some examples file in this video. However, I can not to find corresponding file in the new version of Optimus(https://github.com/MolecularCartography/Optimus#knime-basics), such as, groupmapping file and stub.txt.Could you give me this information? Thanks a lot.
huali