[Feature]: Add tree quality as iteration metric for RAxML-NG phylogenies

[MillironX]

Summary

Allow for phylogenetic tree quality to be the criteria for how much time to spend on bootstrapping trees, rather than just the number of trees.

Added Features

Additional parameters

• --phylogenetic_bootstrap_cutoff
  • type: float
  • default: 0.03
  • Will be passed to the --bs-cutoff parameter of RAxML-NG

More Info

Context

There is currently no way to determine if a phylogenetic tree is "good" before the pipeline is finished, and if it isn't "good," the only way to make it better is to re-run the pipeline with a higher value of --phylogenetic_bootstraps, which wastes all of the computing power used on the last run, and still doesn't guarantee "goodness."

Possible implementation

Rewrite the phylogenetic_tree process to

1. Run raxml-ng --all with the --phylogenetic_bootstraps parameter passed to --bs-trees option
2. Check for convergence at the --phylogenetic_bootstrap_cutoff level using raxml-ng --bsconverge
3. If 2 has not reached convergence, then
   1. Increment the random seed
   2. Go to 1, either using the Nextflow feedback loop pattern (preferred), or a shell script
4. If 2 has reached convergence, then output and exit

[MillironX]

Fixed by #20