they're only deprecated in the sense that "if there is a better way don't use them"
Since I'm just working on the
data_meta filter the discussion is really helpful. Currently only metadata given in the form of text or lists is used properly. Anything else, like dict, orderedDict, or even files is currently ignored (or better: I don't know what would happen). For the files my guess would be that the filenames are listed.
Is there somewhere a list of possibilities in which data structures metadata should be encoded?
Seems to be int, string, list, Ordered dict (which are MetadataParameter) and file names (which are metadata.FileParameter ) .. so one can differentiate them.
Question is if there is an easy way to address the data of interest
How about the following:
For the latter case a combination of the regexp and multiple_splitter filters the the relevant pieces of the info can be extracted.
One thing that one needs to keep in mind is that usually only a part of large files is considered.
VariantsToTablefunction takes a list of fields from the INFO part of the vcf header. I'd rather not store all of that in database metadata, so a metadata file makes sense to me, but (as discussed) we don't (as far as I can tell) have an option to populate e.g. a multi-select from metadata stored in a file
Pillowpython's imaging library as a requirement for one of the tools and planemo tests fail with an error
ImportError: No module named PIL. My understanding is
Pillowis not available in
bioconda. Is there a way to use