Hi! I was wondering if it would be useful to code ...
# genephylomodeler
l
Hi! I was wondering if it would be useful to code all the nf-core modules (for hyphy at least) that are included in the pipeline? I have started with (only) BUSTED for now, but I think it would be nice so that they can be integrated in the pipeline directly, which reduces the amount of work for review at release time, as well as versions updates and the like. Once the first module is done it should be fairly quick to do the others as the test files and large parts of the modules would be exactly the same. I mention this notably because I recently tried to run the pipeline for some GARD analyses, and it failed because the GARD local module is implemented with "process_single", which limits it to 1 CPU and 4h of runtime. Most analyses (at least for the 15 I tried to run) far exceed that. I know it's possible to update this via config, but I think it would be easier to just have a process label that is appropriate for most use cases. On another note, I'm waiting for a review for a conda package so I can then implement a module for Biopp, a library that allows for running selection models like the ones in codeml (except faster and with easier access to parametrization), as I would like to also add it to the pipeline.