TODO

This is an (incomplete) list of todos for the Pipeline:

Documentation:
- new 'serial=threads' option


general:
- change submission system to cluster profiles instead of cluster config files.
- be more verbose on quiet runs to catch some case were snakemake wont run (eg. incomplete files, error in CSV data file)
- add setup rules to cluster config
setup:
- sometimes genome downloads fail (time-out etc.) meaning that the --setup step has to be run again. This should be avoided. (DONE)
- be more clear which genome (sometimes there are multiple assemblies) should be downloaded. (DONE)
- if genomes are removed from the data.csv they are not removed by setup or add-genomes
- add possiblity to use ENTREZ key

busco:
- currently busco 3 is used. Providing the possibility to use busco4 would be good.
- busco fails with Myriosclerotinia_sulcatula

tree:
- switch phylobayes to MPI version
- At the moment iqtree is run to create models for different genes which are used in raxml. Not all model names are the same in iqtree and raxml. This needs to be better tested so that it works in all cases with raxml.
- It would be nice to avoid recalculating models for gene trees and conatenated trees with iqtree. This is already done before for raxml, however not used for iqtree. This would save computation time.