I think provided_lineages_file is no longer optional

[taylorreiter]

I ran charcoal on some de novo bins without using provided lineages in the conf file, and I got this error

Building DAG of jobs...
MissingInputException in line 370 of /home/tereiter/github/2021-metapangenome-example/.snakemake/conda/e8744e4d964b404a29c4b867cfc52b25/lib/python3.9/site-packages/charcoal/Snakefile:
Missing input files for rule compare_taxonomy_single_wc:

Looking at that rule and the rest of the snakefile, I didn't see anything that made that input optional on the snakemake side of things

https://github.com/dib-lab/charcoal/blob/latest/charcoal/Snakefile#L375

rule compare_taxonomy_single_wc:
    input:
        json = stage1_dir + '/{g}.contigs-tax.json',
        matches_csv = stage1_dir + '/{g}.matches.csv',
        lineages = config['lineages_csv'],
        provided_lineages = provided_lineages_file,
        databases = config['gather_db'],
        genome_list = genome_list_file,