Simplify configuration of accession as metadata id column#2021
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victorlin wants to merge 6 commits into
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Simplify configuration of accession as metadata id column#2021victorlin wants to merge 6 commits into
accession as metadata id column#2021victorlin wants to merge 6 commits into
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Mention that values must be unique, and --metadata-id-columns can be used to use other columns.
Reflect the changes in "Prefer `strain` over `name` as sequence ID field" (6064fa2).
Prefer a new explicit 'id' column to represent unique identifier, instead of 'strain' and 'name' which have historically been associated with non-unique columns from some data sources.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #2021 +/- ##
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- Coverage 72.96% 72.96% -0.01%
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Files 85 85
Lines 10732 10730 -2
Branches 2102 2100 -2
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Allow explicitly naming the id column in merged metadata output, instead of always using the first input's id column, so workflows can use a standard id column name regardless of inputs.
Allow --metadata and --sequences to accept a single input instead of requiring at least two, since augur merge is also used as a general entry point for standardization even when no actual merge across inputs is needed.
Follow-up to "Read FASTA files with SeqKit directly" (44b72fe) which is really more of a workaround than a fix.
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accession as metadata id column
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Description of proposed changes
This PR's commits revolve around a common goal of simplifying metadata id column handling in workflows. See #1780 (comment) for context.
Related issue(s)
accessionas metadata id column #1780Checklist