Remove the 2 required string inputs from the TheiaCov_FASTA_Batch_PHB workflow, to ease usage of this workflow. These inputs are not really "used" in the workflow. They are simply passed into the sample-level Terra table TSV that is uploaded to Terra in the final step of the workflow. So what the user provides as a single string, will be overwritten for all samples in the batch, which could lead to overwriting existing values (in the scenario where the user doesn't want to overwrite them, or doesn't know they are being overwritten!)
seq_method
input_assembly_method
I've started PR #319 which will address this.
We can also use this PR to add any other improvements/bug fixes to the theiacov_fasta_batch_phb workflow. Please let me know if you have or hear feedback about running this workflow!
:books: Context
When I went to run this workflow, I initially thought these inputs were String arrays, so I got many errors when trying to provide an array of strings (with the mindset that I'm analyzing FASTA files that were generated with different sequencing platforms and assembly methods)
:chart_with_upwards_trend: Desired Behavior
remove these as required inputs, as in...completely remove them from the workflow. I can't think of a scenario where we would want the workflow to manipulate/overwrite these columns. Probably better for the user to just update their Terra table manually via the typical TSV upload.
:cool:
:pushpin: Explain the Request
Remove the 2 required string inputs from the TheiaCov_FASTA_Batch_PHB workflow, to ease usage of this workflow. These inputs are not really "used" in the workflow. They are simply passed into the sample-level Terra table TSV that is uploaded to Terra in the final step of the workflow. So what the user provides as a single string, will be overwritten for all samples in the batch, which could lead to overwriting existing values (in the scenario where the user doesn't want to overwrite them, or doesn't know they are being overwritten!)
seq_methodinput_assembly_methodI've started PR #319 which will address this.
We can also use this PR to add any other improvements/bug fixes to the theiacov_fasta_batch_phb workflow. Please let me know if you have or hear feedback about running this workflow!
:books: Context
When I went to run this workflow, I initially thought these inputs were String arrays, so I got many errors when trying to provide an array of strings (with the mindset that I'm analyzing FASTA files that were generated with different sequencing platforms and assembly methods)
:chart_with_upwards_trend: Desired Behavior
remove these as required inputs, as in...completely remove them from the workflow. I can't think of a scenario where we would want the workflow to manipulate/overwrite these columns. Probably better for the user to just update their Terra table manually via the typical TSV upload.
:information_source: Additional Information