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Use full Nextclade names for all gene segments
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Not all gene segments define shorter aliases (e.g., "flu_h3n2_ha"), so
we need to use the full names (e.g., "nextstrain/flu/h3n2/ha") to
download each dataset.
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huddlej committed Oct 15, 2024
1 parent 3780fc0 commit 582236f
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion profiles/nextclade/run-nextclade.smk
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ rule get_nextclade_dataset_for_lineage_and_segment:
shell:
"""
nextclade3 dataset get \
-n flu_{wildcards.lineage}_{wildcards.segment} \
-n 'nextstrain/flu/{wildcards.lineage}/{wildcards.segment}' \
--output-dir {output.nextclade_dir}
"""

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