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Use only the 21L sequence from references
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data/references_sequences.fasta contains both `Wuhan/Hu-1/2019` and
`21L`. The aligned input is expected to contain `Wuhan/Hu-1/2019` so the
merging with references_sequences.fasta is really only for 21L.
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victorlin committed Oct 1, 2024
1 parent 41e2e8f commit 567279a
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk
Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,8 @@ rule gisaid_21L_aligned:
exec 2> {log:q}
< {input.references:q} \
zstd \
seqkit grep --by-name --pattern 21L \
| zstd \
> {output.aligned}
< {input.aligned:q} \
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