Gibs
**Snakemake version** 7.8.1 **Describe the bug** When a rule has a wildcard in the path to an external script, `--report` is unable to parse the script path for inclusion. **Logs**...
Snakemake version: 7.3.0 The help for `--default-resources` states that arguments should be of the form `NAME=INT` (name=integer). https://github.com/snakemake/snakemake/blob/cc6c9986271738dfa8394fc45720a4d756af9d0a/snakemake/__init__.py#L1201-L1217 However, to me it seems that Snakemake is perfectly happy taking a...
I'd like to use Empress in a Snakemake pipeline (see below) but I'm running into an annoying issue. If my understanding is correct (which it could very well not be),...
I have a branch for this on [DEICODE](https://github.com/gibsramen/DEICODE/tree/feature_mat) but it would be nice to have in gemelli as well. Useful for me when working on CoRASCON and probably others as...
Is there a way to easily tie which feature came from which modality at the moment? As far as I can tell, the current implementation stores all features across tables...
Modifies main Joint-RPCA code slightly to now save a mapping of which feature is from which modality (table). Adds some code to create a simple network using NetworkX. @cameronmartino What...
Came up during discussion with @fedarko Might be useful to allow the user to specify a regular expression for which to search the feature space. This should hopefully allow users...
One thing I noticed when playing around with feature balances is that the auto-scaling y-axis can sometimes mask the effect size of log-ratio differences. For example, a balance with more...
Spun-off from #266 Lower priority but still might be nice to have in the future.