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Annotate GIHSN strains #196

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joverlee521 opened this issue Nov 12, 2024 · 0 comments · May be fixed by #198
Open

Annotate GIHSN strains #196

joverlee521 opened this issue Nov 12, 2024 · 0 comments · May be fixed by #198
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enhancement New feature or request

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joverlee521 commented Nov 12, 2024 •
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Strains from the Global Influenza Hospital Surveillance Network (GIHSN) have GIHSN in the strain name. We should add a rule to add a GIHSN column to the metadata to indicate whether the label is in the strain name.

I'm imagining this to be a step before/after the rule to annotate the reference strains.
@joverlee521 joverlee521 added the enhancement New feature or request label Nov 12, 2024
@joverlee521 joverlee521 changed the title Annotate GISHN strains Annotate GIHSN strains Nov 20, 2024
joverlee521 added a commit that referenced this issue Nov 20, 2024
@joverlee521
Add rule to annotate GIHSN samples
743e77d 
Adds a new `gihsn_sample` column to the metadata.tsv to indicate
whether "GIHSN" was found in the `strain`.

Resolves <#196>
@joverlee521 joverlee521 self-assigned this Nov 20, 2024
joverlee521 added a commit that referenced this issue Nov 20, 2024
@joverlee521
Add rule to annotate GIHSN samples
dfcd671 
Adds a new `gihsn_sample` column to the metadata to indicate whether
"GIHSN" was found in the `strain` as proxy for whether the sample came
from the Global Influenza Hospital Surveillance Network (GIHSN).
Follows the existing pattern of using `True` and `False` boolean values.

Resolves <#196>
@joverlee521 joverlee521 linked a pull request Nov 20, 2024 that will close this issue
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Add rule to annotate GIHSN samples nextstrain/seasonal-flu
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