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Update Nextclade workflow to use augur merge/rename #21

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genehack opened this issue Nov 26, 2024 · 0 comments · Fixed by #32
Closed

Update Nextclade workflow to use augur merge/rename #21

genehack opened this issue Nov 26, 2024 · 0 comments · Fixed by #32
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Since you're making changes here, consider updating the join_metadata_and_nextclade rule to use augur rename and augur merge (see nextstrain/pathogen-repo-guide#67)

Originally posted by @joverlee521 in #20 (comment)
@genehack genehack mentioned this issue Nov 26, 2024
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@genehack genehack self-assigned this Dec 9, 2024
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Move nextclade field map into config [#21]
2239f4a
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Use augur curate to generate intermediate Nextclade metadata file [#21]
0d6acd2
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Use augur merge to unify nextclade and NCBI metadata [#21]
3dddc12
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Remove an extraneous temp() that Snakemake just started complaining a…
c1c19ac 
…bout [#21]
@genehack genehack mentioned this issue Dec 20, 2024
Merged
1 task
genehack added a commit that referenced this issue Jan 9, 2025
@genehack
Use augur merge to unify nextclade and NCBI metadata [#21]
b156c6b
genehack added a commit that referenced this issue Jan 9, 2025
@genehack
Remove an extraneous temp() that Snakemake just started complaining a…
6a4b959 
…bout [#21]
genehack added a commit that referenced this issue Jan 9, 2025
@genehack
Merge pull request #32 from nextstrain/update-nextclade-rules-in-inge…
b451c59 
…st-21

Update nextclade rules in ingest [#21]
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Update nextclade rules in ingest [#21] nextstrain/yellow-fever
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@genehack