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Use augur merge for sequences
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Use our own tooling designed for this type of operation.
victorlin committed Dec 7, 2024
1 parent b92c80c commit 2a840c3
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions phylogenetic/rules/merge_sequences_usvi.smk
Original file line number Diff line number Diff line change
@@ -57,10 +57,10 @@ rule append_usvi:
metadata = "data/metadata_all.tsv"
shell:
"""
seqkit rmdup {input.usvi_sequences} {input.sequences} > {output.sequences}
augur merge \
--metadata ingest={input.metadata} usvi={input.usvi_metadata} \
--sequences ingest={input.sequences} usvi={input.usvi_sequences}
--metadata-id-columns accession \
--output-metadata {output.metadata}
--output-metadata {output.metadata} \
--output-sequences {output.sequences}
"""

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