Open joverlee521 opened 1 year ago
I lean toward possible solution 2, but I'm probably missing the historical context.
My guess is that this was removed when we tried to pare down what we were bringing in from Nextclade to keep it to only things that were of most use. I imagine it won't come back and it's hard for me to imagine that users are supplying their own value here. However @rneher & @corneliusroemer might be able to provide a bit more context just in case we're missing anything.
This predates me, I can't really comment here.
Context
@huddlej's response to a discussion question prompted me to take a closer look at the
diagnostics
rule/script. I wanted to understand how the hard-coded params were used in the script: https://github.com/nextstrain/ncov/blob/44ab71ab3bace68c59bd5c688587e6e30a4a4fc4/workflow/snakemake_rules/main_workflow.smk#L536-L539I saw that the
snp_clusters
param is only relevant when there is asnp_clusters
column within the input metadata file.https://github.com/nextstrain/ncov/blob/44ab71ab3bace68c59bd5c688587e6e30a4a4fc4/scripts/diagnostic.py#L84-L87
This input metadata file is generated by the
join-metadata-and-clades
script, which does not add asnp_clusters
column. Only the following columns from Nextclade are included in the metadata file:https://github.com/nextstrain/ncov/blob/44ab71ab3bace68c59bd5c688587e6e30a4a4fc4/scripts/join-metadata-and-clades.py#L19-L41
It seems like the
snp_clusters
param is unused unless users add the column to their own metadata outside the workflow.snp_clusters
used to be included as a column in thencov-ingest
produced metadata file, but it has been removed. I think the presence of an unused param here can cause confusion for users (it definitely confused me!).Possible solution
I'm not familiar with the diagnosis rule so I wanted to ask what would be an appropriate action here.
diagnostics
rule that thesnp_clusters
is only kept for backwards compatibility, but it is not used in the latest version of the workflow.snp_clusters
param from thediagnostics
rule.diagnostics
script to checkQC_snp_clusters != "bad"
instead of the number of SNP clusters.