Currently, the include gbff and include gff optional inputs are exposed to users in the Snippy_Streamline workflow. These files are not output to the data table (only the cloud storage). By using the gbff (gbk) file as the reference, the SNPs that are identified in the workflow will be annotated with the gbff information (CDS name etc).
:books: Context
Knowing the CDS of the SNP is valuable for understanding where in the genome SNPs are occurring. This complements the shared SNPs task (https://github.com/theiagen/public_health_bioinformatics/pull/291) for identifying the shared SNPs. Currently, a user would only know the context of those SNPs if they input their own reference rather than using ReferenceSeeker.
:chart_with_upwards_trend: Desired Behavior
Output the gbff file to the Terra table
Maybe comment out the include_gff optional input as this probably isn't useful in Snippy_Streamline
Use the gbff file as the preferred reference file when include_gbff is used
:cool:
:pushpin: Explain the Request
Currently, the
include gbffandinclude gffoptional inputs are exposed to users in the Snippy_Streamline workflow. These files are not output to the data table (only the cloud storage). By using the gbff (gbk) file as the reference, the SNPs that are identified in the workflow will be annotated with the gbff information (CDS name etc).:books: Context
Knowing the CDS of the SNP is valuable for understanding where in the genome SNPs are occurring. This complements the shared SNPs task (https://github.com/theiagen/public_health_bioinformatics/pull/291) for identifying the shared SNPs. Currently, a user would only know the context of those SNPs if they input their own reference rather than using ReferenceSeeker.
:chart_with_upwards_trend: Desired Behavior
include_gffoptional input as this probably isn't useful in Snippy_Streamlineinclude_gbffis usedinclude_gbff= true by default:information_source: Additional Information