NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
This PR simplifies the annotation module substantially. We now only obtain the UniProt return fields for the annotations used by COGEQC for MCL selection (InterPro domain and OMA orthology group ID). The README, usage.md and outputs.md documentation files are updated correspondingly.
Additionally, in the README we now:
Highlight that due to changes in NovelTree's dependencies, NovelTree no longer is unfortunately no longer compatible with Apple silicon.
Provide simple examples of how to specify available resources (e.g. number CPUs, memory) when running NovelTree. Without doing so, users may run into errors thrown by Nextflow due to incompatible process specifications for certain modules.
This PR simplifies the annotation module substantially. We now only obtain the UniProt return fields for the annotations used by
COGEQCfor MCL selection (InterPro domain and OMA orthology group ID). TheREADME,usage.mdandoutputs.mddocumentation files are updated correspondingly.Additionally, in the
READMEwe now:NovelTreeno longer is unfortunately no longer compatible with Apple silicon.NovelTree. Without doing so, users may run into errors thrown by Nextflow due to incompatible process specifications for certain modules.