From ea07025643dd275f8dcf3cea7667ad0983d508af Mon Sep 17 00:00:00 2001
From: Richard Neher <richard.neher@unibas.ch>
Date: Wed, 23 Aug 2023 18:28:07 +0200
Subject: [PATCH] add dummy yam files, fix rule name

---
 config/yam/ha/subclades.tsv         | 12 ++++++++++++
 config/yam/na/subclades.tsv         |  0
 workflow/snakemake_rules/core.smk   |  6 +++---
 workflow/snakemake_rules/export.smk |  5 ++++-
 4 files changed, 19 insertions(+), 4 deletions(-)
 create mode 100644 config/yam/ha/subclades.tsv
 create mode 100644 config/yam/na/subclades.tsv

diff --git a/config/yam/ha/subclades.tsv b/config/yam/ha/subclades.tsv
new file mode 100644
index 00000000..780c3f2a
--- /dev/null
+++ b/config/yam/ha/subclades.tsv
@@ -0,0 +1,12 @@
+clade	gene	site	alt
+Y1	SigPep	1	M
+Y2	HA1	48	K
+Y2	HA1	108	A
+Y2	HA1	181	A
+Y3	HA1	116	K
+Y3	HA1	150	I
+Y3	HA1	165	Y
+Y3	HA1	202	S
+Y3	HA1	229	D
+Y3	HA1	298	E
+Y3	HA1	312	K
diff --git a/config/yam/na/subclades.tsv b/config/yam/na/subclades.tsv
new file mode 100644
index 00000000..e69de29b
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
index 75df83db..0cc23e2b 100644
--- a/workflow/snakemake_rules/core.smk
+++ b/workflow/snakemake_rules/core.smk
@@ -364,7 +364,7 @@ rule clades:
         """
 
 # Determine subclades for na and ha.
-rule subclade:
+rule subclades:
     input:
         tree = build_dir + "/{build_name}/{segment}/tree.nwk",
         nt_muts = build_dir + "/{build_name}/{segment}/nt-muts.json",
@@ -377,9 +377,9 @@ rule subclade:
         label_name = "Subclade",
     conda: "../envs/nextstrain.yaml"
     benchmark:
-        "benchmarks/clades_{build_name}.txt"
+        "benchmarks/clades_{build_name}_{segment}.txt"
     log:
-        "logs/clades_{build_name}.txt"
+        "logs/clades_{build_name}_{segment}.txt"
     shell:
         """
         augur clades \
diff --git a/workflow/snakemake_rules/export.smk b/workflow/snakemake_rules/export.smk
index aded8b38..2115287a 100644
--- a/workflow/snakemake_rules/export.smk
+++ b/workflow/snakemake_rules/export.smk
@@ -10,7 +10,6 @@ def _get_node_data_by_wildcards(wildcards):
         rules.ancestral.output.node_data,
         rules.translate.output.node_data,
         rules.clades.output.node_data,
-        rules.subclades.output.node_data,
         rules.traits.output.node_data,
         rules.annotate_epiweeks.output.node_data,
         rules.annotate_recency_of_submissions.output.node_data,
@@ -21,6 +20,10 @@ def _get_node_data_by_wildcards(wildcards):
     if _get_build_distance_map_config(wildcards) is not None:
         inputs.append(rules.distances.output.distances)
 
+
+    if config["builds"][wildcards.build_name].get('subclades', False):
+        inputs.append(rules.subclades.output.node_data)
+
     if config["builds"][wildcards.build_name].get('enable_titer_models', False) and wildcards.segment == 'ha':
         for collection in config["builds"][wildcards.build_name]["titer_collections"]:
             inputs.append(rules.titers_sub.output.titers_model.format(titer_collection=collection["name"], **wildcards_dict))