SNVPhyl no-longer works in Galaxy

[apetkau]

Describe the bug

Installing the SNVPhyl pipeline tools and running the workflow (version 1.2.2) no-longer works in Galaxy (tested on Galaxy 20.05 and 21.01). The following exception is generated:

ca.corefacility.bioinformatics.irida.exceptions.WorkflowException: GalaxyResponseException{status=400, responseBody={"err_msg": {"sec_filter|select_genotype": "para
meter 'select_genotype': an invalid option ('__none__') was selected (valid options: het,^het,^miss,miss,hom,^hom) Using default: 'None'."}, "err_code": 0, "err_dat
a": {"9": {"sec_filter|select_genotype": "parameter 'select_genotype': an invalid option ('__none__') was selected (valid options: het,^het,^miss,miss,hom,^hom) Usi
ng default: 'None'."}}}, errorMessage=null, errorCode=null, traceback=null}

Steps to reproduce the problem

What were you doing when you encountered the problem?

1. Install the SNVPhyl tool suite
2. Run the SNVPhyl pipeline.
3. The above exception occurs.

Expected behaviour

I expected the pipeline to finish successfully.

Additional context

None.

[apetkau]

It looks like the revision used by the workflow for the bcftools_view (c4a9b38b435d) is no longer available in Galaxy and has been replaced with https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_view/98d5499ead46. This updates one of the parameters for the workflow (select_genotype) - https://github.com/galaxyproject/tools-iuc/commit/8f0dacb44516206751262495e6a6de22ae312572

So, this tool will likely need to be updated for SNVPhyl since you can no-longer install the proper version of this tool in Galaxy.

[tom114]

Fixed in #1035