From 2a840c34c3389fa6798ee0383008767ecd6d5c4c Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 6 Dec 2024 17:19:08 -0800
Subject: [PATCH] Use augur merge for sequences

Use our own tooling designed for this type of operation.
---
 phylogenetic/rules/merge_sequences_usvi.smk | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/phylogenetic/rules/merge_sequences_usvi.smk b/phylogenetic/rules/merge_sequences_usvi.smk
index ffc7a50..1b6c838 100644
--- a/phylogenetic/rules/merge_sequences_usvi.smk
+++ b/phylogenetic/rules/merge_sequences_usvi.smk
@@ -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}
         """
\ No newline at end of file