Ok I'm done with 9 out of the 10 modules included ...
# genephylomodelerl
Lea Picard (leapfroggie_)
08/27/2026, 8:04 PMOk I'm done with 9 out of the 10 modules included in GPM, just missing RELAX as I've never used it so I'm not sure how to format the foreground vs reference tags (so I can build a test for the module)
Also idk if other modules should be made (PRIME etc)?
I guess one for DRHIP would be good at least?
Lea Picard (leapfroggie_)
08/27/2026, 8:09 PMthough I'm not sure if DRHIP would work with the directory structure of results in nf-core - the results are indeed in folders with the name of the method but these are lowercase and not uppercase, don't know how strictly DRHIP enforces the name match
d
Danielle
09/04/2026, 3:54 PMill make any changes you need in drhip, just let me know.
Danielle
09/04/2026, 3:55 PMex relax module if helpful: github.com/veg/CAPHEINE/…/relax
and drhip: github.com/veg/CAPHEINE/…/drhip
Danielle
09/04/2026, 3:55 PMfeel free to ping
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Lea Picard (leapfroggie_)
09/04/2026, 5:12 PMThanks, I did take a look at the modules in CAPHEINE but my problem is related to the format of
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val(foreground_tag)
val(reference_tag)d
Danielle
09/04/2026, 5:24 PMoh i see, misunderstood initially. some things to help, see: github.com/veg/CAPHEINE/…/labeltree where hyphy adds these little annotation on nodes in newick and help.datamonkey.org/methods/relax.html .. so you can use regex or list to label nodes 'foreground' vs 'background' and then the labels are what you pass to relax.
Danielle
09/04/2026, 5:26 PMso relax test will want an already labeled tree, but actually using relax in a wf youll want to let ppl label their trees also
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Lea Picard (leapfroggie_)
09/04/2026, 6:34 PMAh so there should probably be a module for labeltree upstream of relax then, right?
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Lea Picard (leapfroggie_)
09/04/2026, 6:39 PMregarding upstream/downstream logic for the pipeline itself as well (not gonna touch it for now but just reflecting on it), should we also run the fragments obtained from GARD through the other methods
ie let's say user wants to do GARD BUSTED and FUBAR on geneX, all 3 of those methods are run but GARD identifies one breakpoint, it would make sense to run BUSTED and FUBAR again on both fragments, wouldn't it?
d
Danielle
09/04/2026, 6:42 PMif gard finds breakpoints, i would run only on the breakpoint trees for the other methods.
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