When running the workflow in OrthoFinder mode (use_orthofisher: False), it dies with an error message if you remove the orthofisher_hmmer_files from the config file even though those files are irrelevant for a run with OrthoFinder. Would be nice if orthofisher_hmmer_files don't have to be defined for such runs.
Error message as follows:
Running phyloflow...
snakemake --snakefile=/home/ubuntu/phaeoexplorer/input_data/phyloflow/phyloflow/workflow/Snakefile --use-conda --cores=30 --directory=.
KeyError in line 15 of /home/ubuntu/phaeoexplorer/input_data/phyloflow/phyloflow/workflow/rules/orthofisher.smk:
'orthofisher_hmmer_files'
File "/home/ubuntu/phaeoexplorer/input_data/phyloflow/phyloflow/workflow/Snakefile", line 34, in <module>
File "/home/ubuntu/phaeoexplorer/input_data/phyloflow/phyloflow/workflow/rules/orthofisher.smk", line 15, in <module>
When running the workflow in OrthoFinder mode (use_orthofisher: False), it dies with an error message if you remove the orthofisher_hmmer_files from the config file even though those files are irrelevant for a run with OrthoFinder. Would be nice if orthofisher_hmmer_files don't have to be defined for such runs.
Error message as follows: