Nick Dimonaco comments

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                                            Nick Dimonaco

Diversity of input folder names

Hi. I am currently looking into making it easier and more 'user-driven' for selecting input files and hopefully, I will have some progress on this soon. Thanks for the request.

Diversity of input folder names

Sorry for the delay. Please try v1.2.0 with the "-af" option to provide the alternative filename: `StORF-Reporter -anno Bakta Out_Dir -p ./Ecoli_23_BAKTA -af Ecoli_23`

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Hi both, I think it would be wrong to assume that these smaller sequences are going to always be 'incomplete' versions of the larger ones. Many genes share domains etc....

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

@gtonkinhill - Could I ask another question. If for example we had a gene family as described above but that shorter sequence we see is from the same genome (think,...

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

So for each gene family/ group, you use the longest fragment (or pick randomly if two of the same size) for the MSA. This makes sense as I have been...

Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

Will test it out. Thanks

Models not loading for test run

I have a similar error from the new v1.1.0: ``` [02/20/2025 05:30:53 PM] INFO: Running CheckM2 version [1.1.0](https://github.com/chklovski/CheckM2/releases/tag/1.1.0) [02/20/2025 05:30:53 PM] INFO: Running quality prediction workflow with 4 threads. [02/20/2025...