Update glossary and graphviz for repo/workflows #191
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victorlin
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Mar 4, 2024
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Thanks for starting this PR, these changes are much needed! The suggestions below are based on the idea of going full send in the direction of multi-workflow pathogen repos, instead of keeping existing wording that assumes each pathogen repo = 1 phylo workflow. This means drawing clear boundaries around the types of workflows to align with pathogen-repo-guide, and at least acknowledging the presence of ingest/nextclade workflows if not walking through them in detail like the phylo workflow.
With the push for pathogen repos to adhere to the pathogen-repo-guide, the glossary and graphviz for repositories and workflows need to be updated. This will also make it easier to use standardized terminology in the upcoming ingest tutorials.
Keep the term `workflow` general and link out to individual workflow terms that summarize their uses. Based on suggestion from @victorlin in review #191 (comment)
Updating term references that used "workflow" to "phylogenetic workflow" where appropriate to match new definitions defined in previous commit.
Based on @victorlin's suggestion in review #191 (comment) This will pave the way for the addition of ingest workflow tutorials in the near future.
Keep the term `dataset` general and link out to individual dataset terms that summarize their uses. Based on suggestion from @victorlin in review #191 (comment)
Updating term references that used "dataset" to "phylogenetic dataset" where appropriate to match new definitions defined in previous commit.
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Major updates after initial feedback from @victorlin:
I'm planning to add the ingest tutorials in a separate branch based on these changes so they can link back to these new terms. |
j23414
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Mar 22, 2024
victorlin
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Mar 27, 2024
Co-authored-by: Victor Lin <[email protected]>
Originally suggested to create individual terms for each build (phylogenetic/ingest/Nextclade) to match the individual terms for "workflow" and "dataset", but seeing the terms written out made it seem like overkill. Instead, just adding the aliases to clarify the term covers all three types of builds, as suggested by @victorlin in review.¹ ¹ #191 (comment)
The colloquial term "Nextstrain workflow" is usually referring to a phylogenetic workflow since we used to only have the phylogenetic workflow.
victorlin
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Mar 28, 2024
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This is great! Nice work. |
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Description of proposed changes
With the push for pathogen repos to adhere to the pathogen-repo-guide, the glossary and graphviz for repositories and workflows need to be updated.
This will also make it easier to standardize terminology in the upcoming ingest tutorials.
Related issue(s)
Resolves #190
Checklist