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Add ingest #10
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Add ingest #10
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866abd6
Copy ingest from pathogen-repo-template
kimandrews 8555df3
git subrepo clone (merge) https://github.com/nextstrain/ingest ingest…
kimandrews e830f65
Add ingest config parameters
kimandrews 375d9ec
Remove Entrez rules and config parameters
kimandrews 9f6cc30
Remove nextclade-related rules
kimandrews 7e10c4b
Remove ingest/profiles
kimandrews 07416e6
Add abbr_authors to metadata_columns
kimandrews 0fca27e
Fix typo in ingest/rules/curate.smk
kimandrews 9ebfebc
Add NCBI Datasets "virus-name" field
kimandrews 9afc28f
Remove nextclade_field_map.tsv
kimandrews c9dfc64
Don't replace empty strain names
kimandrews d2737ed
Renamed "config" directory to "defaults"
kimandrews 6976bd4
ingest/README.md: remove Profiles, change config to defaults
kimandrews 3fb3e9e
Remove nextclade from Snakefile
kimandrews 90a70cd
Remove Entrez from docstring of fetch_from_ncbi.smk
kimandrews da3c325
git subrepo pull (merge) --force ingest/vendored
kimandrews e766152
Update Changelog
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ingest/README.md: remove Profiles, change config to defaults
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It also includes
all_metadata.tsv
.In phylo workflows we have
{data,results,auspice}
and it's understood that the files inresults
can be numerous and change frequently with workflow updates. For ingest we only have{data,results}
. My understanding is that more complex ingest workflows will populateresults
with many files. So maybe we could change the wording here to indicate that of the files inresults
these two are the ones that should be used for downstream analysis.There was a problem hiding this comment.
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Ah, the
all_metadata.tsv
looks like an intermediate data file, not the final resultmetadata.tsv
.@kimandrews, you can change the path from
results/all_metadata.tsv
todata/all_metadata.tsv
so there's less confusion on what the final output files should be (e.g.results/sequences.fasta
andresults/metadata.tsv
.measles/ingest/rules/curate.smk
Line 64 in 90a70cd
measles/ingest/rules/curate.smk
Lines 119 to 123 in 90a70cd
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Done in f3fe0c1