From c8547a293caae696886ba75135b92a4ddf3857c0 Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Tue, 30 Apr 2024 10:49:58 -0700
Subject: [PATCH] fixup: use include file in `augur filter`

---
 phylogenetic/rules/prepare_sequences.smk      | 1 +
 phylogenetic/rules/prepare_sequences_N450.smk | 1 +
 2 files changed, 2 insertions(+)

diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
index 508fcc7..6d5bf85 100644
--- a/phylogenetic/rules/prepare_sequences.smk
+++ b/phylogenetic/rules/prepare_sequences.smk
@@ -59,6 +59,7 @@ rule filter:
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
+            --include {input.include} \
             --output {output.sequences} \
             --group-by {params.group_by} \
             --sequences-per-group {params.sequences_per_group} \
diff --git a/phylogenetic/rules/prepare_sequences_N450.smk b/phylogenetic/rules/prepare_sequences_N450.smk
index 7f91da8..d009c25 100644
--- a/phylogenetic/rules/prepare_sequences_N450.smk
+++ b/phylogenetic/rules/prepare_sequences_N450.smk
@@ -51,6 +51,7 @@ rule filter_N450:
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
+            --include {input.include} \
             --output {output.sequences} \
             --group-by {params.group_by} \
             --subsample-max-sequences {params.subsample_max_sequences} \