From c433ecb38b07476d66fe3012ec08302d01e0937c Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Tue, 4 Jun 2024 13:45:04 -0700
Subject: [PATCH] Fixup: lower the ENV gene min-length

---
 phylogenetic/defaults/config_zika.yaml   | 4 +++-
 phylogenetic/rules/prepare_sequences.smk | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/phylogenetic/defaults/config_zika.yaml b/phylogenetic/defaults/config_zika.yaml
index d25c2c6..7a08ec9 100644
--- a/phylogenetic/defaults/config_zika.yaml
+++ b/phylogenetic/defaults/config_zika.yaml
@@ -10,7 +10,9 @@ filter:
   group_by: "country year month"
   sequences_per_group: 40
   min_date: 2012
-  min_length: 5385
+  min_length:
+    genome: 5385
+    ENV: 1000
 
 refine:
   coalescent: "opt"
diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
index 4549634..a749414 100644
--- a/phylogenetic/rules/prepare_sequences.smk
+++ b/phylogenetic/rules/prepare_sequences.smk
@@ -67,7 +67,7 @@ rule filter:
         group_by = config["filter"]["group_by"],
         sequences_per_group = config["filter"]["sequences_per_group"],
         min_date = config["filter"]["min_date"],
-        min_length = config["filter"]["min_length"],
+        min_length = lambda wildcard: config["filter"]["min_length"][wildcard.gene],
         strain_id = config.get("strain_id_field", "strain"),
     shell:
         """