From 3818fabd51d2384af8637c017be9075587ab6076 Mon Sep 17 00:00:00 2001
From: Trevor Bedford <trevor@bedford.io>
Date: Fri, 28 Jun 2024 16:28:41 -0700
Subject: [PATCH] Move frequencies rule to export.smk

---
 phylogenetic/rules/annotate_phylogeny.smk | 29 -----------------------
 phylogenetic/rules/export.smk             | 25 ++++++++++++++++---
 2 files changed, 22 insertions(+), 32 deletions(-)

diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
index d87627c..61e94b8 100644
--- a/phylogenetic/rules/annotate_phylogeny.smk
+++ b/phylogenetic/rules/annotate_phylogeny.smk
@@ -39,32 +39,3 @@ rule translate:
             --reference-sequence {input.reference} \
             --output {output.node_data} \
         """
-
-rule tip_frequencies:
-    """
-    Estimating KDE frequencies for tips
-    """
-    input:
-        tree = "results/{gene}/tree.nwk",
-        metadata = "data/metadata.tsv"
-    params:
-        strain_id = config["strain_id_field"],
-        min_date = config["tip_frequencies"]["min_date"],
-        max_date = config["tip_frequencies"]["max_date"],
-        narrow_bandwidth = config["tip_frequencies"]["narrow_bandwidth"],
-        wide_bandwidth = config["tip_frequencies"]["wide_bandwidth"]
-    output:
-        tip_freq = "results/{gene}/tip-frequencies.json"
-    shell:
-        """
-        augur frequencies \
-            --method kde \
-            --tree {input.tree} \
-            --metadata {input.metadata} \
-            --metadata-id-columns {params.strain_id} \
-            --min-date {params.min_date} \
-            --max-date {params.max_date} \
-            --narrow-bandwidth {params.narrow_bandwidth} \
-            --wide-bandwidth {params.wide_bandwidth} \
-            --output {output.tip_freq}
-        """
diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
index 32cef95..f6ba939 100644
--- a/phylogenetic/rules/export.smk
+++ b/phylogenetic/rules/export.smk
@@ -34,12 +34,31 @@ rule export:
             --output {output.auspice_json}
         """
 
-rule final_tip_frequencies:
+rule tip_frequencies:
+    """
+    Estimating KDE frequencies for tips
+    """
     input:
-        tip_freq = "results/{gene}/tip-frequencies.json",
+        tree = "results/{gene}/tree.nwk",
+        metadata = "data/metadata.tsv"
+    params:
+        strain_id = config["strain_id_field"],
+        min_date = config["tip_frequencies"]["min_date"],
+        max_date = config["tip_frequencies"]["max_date"],
+        narrow_bandwidth = config["tip_frequencies"]["narrow_bandwidth"],
+        wide_bandwidth = config["tip_frequencies"]["wide_bandwidth"]
     output:
         tip_freq = "auspice/measles_{gene}_tip-frequencies.json"
     shell:
         """
-        cp -f {input.tip_freq} {output.tip_freq}
+        augur frequencies \
+            --method kde \
+            --tree {input.tree} \
+            --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
+            --min-date {params.min_date} \
+            --max-date {params.max_date} \
+            --narrow-bandwidth {params.narrow_bandwidth} \
+            --wide-bandwidth {params.wide_bandwidth} \
+            --output {output.tip_freq}
         """