Use 'time=default' for h5n1-cattle-flu builds

Part of simplifications described in <#70>

This approach avoids using an empty wildcard for time but introduces the need
to have a separate rule to map auspice datasets (which won't have 'time' for h5n1-cattle-flu)
to a filename which does include a time wildcard.

README.md

@@ -59,14 +59,14 @@ nextstrain build \
     . \
         --config s3_src=s3://nextstrain-data/files/workflows/avian-flu/h5n1 \
         -pf \
-        auspice/avian-flu_h5n1-cattle-outbreak_pb2_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_pb1_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_pa_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_ha_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_np_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_na_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_mp_all-time.json \
-        auspice/avian-flu_h5n1-cattle-outbreak_ns_all-time.json
+        auspice/avian-flu_h5n1-cattle-outbreak_pb2.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_pb1.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_pa.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_ha.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_np.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_na.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_mp.json \
+        auspice/avian-flu_h5n1-cattle-outbreak_ns.json
 ```
 
 ## Creating a custom build

Snakefile

@@ -120,7 +120,7 @@ def clock_rate(w):
         'h5n1': {'all-time':'', '2y': clock_rates_h5n1[w.segment]},
         'h7n9': {'all-time':''},
         'h9n2': {'all-time':''},
-        'h5n1-cattle-outbreak': {'all-time': clock_rates_h5n1[w.segment]}
+        'h5n1-cattle-outbreak': {'default': clock_rates_h5n1[w.segment]}
         }
 
     return clock_rate[w.subtype][w.time]
@@ -132,7 +132,7 @@ def clock_rate_std_dev(w):
         'h5n1': {'all-time': '', '2y': '--clock-std-dev 0.00211'},
         'h7n9': {'all-time': ''},
         'h9n2': {'all-time': ''},
-        'h5n1-cattle-outbreak': {'all-time': '--clock-std-dev 0.00211'}
+        'h5n1-cattle-outbreak': {'default': '--clock-std-dev 0.00211'}
         }
 
     return clock_rate_std_dev[w.subtype][w.time]
@@ -399,7 +399,10 @@ def additional_export_config(wildcards):
     return args
 
 rule export:
-    message: "Exporting data files for for auspice"
+    """
+    Export the files into results/ and then use a subsequent rule to move these to the
+    auspice/ directory
+    """
     input:
         tree = refined_tree,
         metadata = metadata_by_wildcards,
@@ -409,7 +412,7 @@ rule export:
         auspice_config = files.auspice_config,
         description = files.description
     output:
-        auspice_json = "auspice/avian-flu_{subtype}_{segment}_{time}.json"
+        auspice_json = "results/avian-flu_{subtype}_{segment}_{time}.json"
     params:
         additional_config = additional_export_config
     shell:
@@ -427,6 +430,46 @@ rule export:
             --output {output.auspice_json}
         """
 
+def auspice_name_to_wildcard_name(wildcards):
+    """
+    Used to link Auspice JSONs filenames to their intermediate filename which includes all wildcards.
+    Examples:
+    1. subtype + segment + time in their filename / URL,
+        e.g. "avian-flu_h5n1_ha_2y.json" (nextstrain.org/avian-flu/h5n1/ha/2y)
+        maps to subtype=h5n1, segment=ha, time=2y
+    2. subtype + segment in their filename / URL,
+        e.g. "avian-flu_h5n1-cattle-outbreak_ha.json" (nextstrain.org/avian-flu/h5n1-cattle-outbreak/ha)
+        maps to subtype=h5n1-cattle-outbreak, segment=ha, time=default
+    """
+    parts = wildcards.parts.split("_")
+    if len(parts)==3:
+        [subtype, segment, time] = parts
+        assert segment!='genome', "Genome builds are not available for this build"
+        return f"results/avian-flu_{subtype}_{segment}_{time}.json"
+    if len(parts)==2:
+        [subtype, segment] = parts
+        assert subtype=='h5n1-cattle-outbreak', "Only h5n1 builds produce an Auspice dataset without a time component in the filename"
+        return f"results/avian-flu_{subtype}_{segment}_default.json"
+    raise Exception("Auspice JSON filename requested with an unexpected number of (underscore-separated) parts")
+
+
+rule rename_auspice_datasets:
+    """
+    This allows us to create files in auspice/ which mirror the intended URL structure rather than
+    the wildcard structure we use in the workflow.
+    """
+    input:
+        json = auspice_name_to_wildcard_name
+    output:
+        json = "auspice/avian-flu_{parts}.json"
+    wildcard_constraints:
+        timepart = ".*"
+    shell:
+        """
+        cp {input.json} {output.json}
+        """
+
+
 rule clean:
     message: "Removing directories: {params}"
     params:

rules/cattle-flu.smk

@@ -11,7 +11,7 @@ rule download_tree:
         dataset="https://data.nextstrain.org/avian-flu_h5n1-cattle-outbreak_genome.json"
     wildcard_constraints:
         subtype="h5n1-cattle-outbreak",
-        time="all-time",
+        time="default",
     shell:
         """
         curl --compressed {params.dataset} -o {output.tree}
@@ -27,7 +27,7 @@ rule prune_tree:
         node_data = "results/tree_{subtype}_{segment}_{time}_outbreak-clade.json",
     wildcard_constraints:
         subtype="h5n1-cattle-outbreak",
-        time="all-time",
+        time="default",
     shell:
         """
         python3 scripts/restrict-via-common-ancestor.py \