allow for non-standardized organisms in TheiaCoV wfs & organism_parameters subwf

https://github.com/theiagen/public_health_bioinformatics/blob/092f19a0f610eb0a01757456932519bbbfe2bbd9/workflows/utilities/wf_organism_parameters.wdl#L254

I tried running a sample with organism set to "measles" to skip all the sars-cov-2 default tasks (pangolin, nextclade, vadr, etc.) and I got an error:

EDIT: this was with v2.0.1 of TheiaCoV_Illumina_PE_PHB workflow

Failed to evaluate 'organism_parameters.standardized_organism' (reason 1 of 1): Evaluating select_first([sc2_org_name, mpox_org_name, wnv_org_name, flu_org_name, rsv_a_org_name, rsv_b_org_name, hiv_v1_org_name, hiv_v2_org_name]) failed: select_first was called with 8 empty values. We needed at least one to be filled.

It's failling on the select_first output String of organism_parameters subworkflow because none of those variables are set & it doesn't allow for user to provide this output as an input.

My expectation was for my input string of "measles" to be passed on as output from the organism_parameters subworkflow, but I guess it make sense that we don't have anything "standardized" for measles. Previous versions of TheiaCoV would allow for skipping organism-specific tasks if the user defined the organism to be something other than the currently-supported organisms.

Can we adjust the organism_parameters workflow to allow for the user-input string to be output as standardized_organism ? or some other solution to allow for analysis of non-SC2/flu/Mpox/RSV/WNV/HIV organisms?

theiagen / public_health_bioinformatics

allow for non-standardized organisms in TheiaCoV wfs & organism_parameters subwf #500