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fixup! Use only the 21L sequence from references
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victorlin committed Sep 30, 2024
1 parent 229eebb commit 5729977
Showing 1 changed file with 1 addition and 5 deletions.
6 changes: 1 addition & 5 deletions nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk
Original file line number Diff line number Diff line change
Expand Up @@ -91,10 +91,8 @@ rule gisaid_21L_aligned:
r"""
exec 2> {log:q}
echo "21L" > reference_ids.txt
< {input.references:q} \
seqkit grep --by-name -f reference_ids.txt \
seqkit grep --by-name --pattern 21L \
| zstd \
> {output.aligned}
Expand All @@ -103,6 +101,4 @@ rule gisaid_21L_aligned:
| seqkit grep --by-name -f {input.strains:q} \
| zstd -T$(({threads} - 2)) \
>> {output.aligned:q}
rm reference_ids.txt
"""

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