Combine color-related rules

Both simplifies the DAG and allows GISAID builds which have GenoFLU colorings to get a nicely ordered set of colours. Note that H9N2 & H7N9 builds, which don't export genoflu metadata, will get colors assigned by the colors rule (because there is a value of "Not assigned (too divergent)" in the metadata TSV) which is then dropped by export.
nextstrain · Feb 26, 2025 · 06c7974 · 06c7974
1 parent 374ed87
commit 06c7974
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Showing 6 changed files with 161 additions and 41 deletions.
diff --git a/Snakefile b/Snakefile
@@ -668,12 +668,25 @@ rule auspice_config:
 
 rule colors:
     input:
-        colors = config['colors']['hardcoded'],
+        metadata = rules.filter.output.metadata,
+        # TODO XXX - d1.1 & cattle-flu used 
+        #         metadata = "results/{subtype}/genome/{time}/metadata.tsv", # Always use the genome metadata, even for segment builds
+        colors = lambda w: get_config('colors', 'hardcoded', w),
+        ordering = lambda w: get_config('colors', 'ordering', w),
+        schemes = lambda w: get_config('colors', 'schemes', w),
     output:
         colors = "results/{subtype}/{segment}/{time}/colors.tsv",
+    params:
+        duplications = lambda w: ["=".join(pair) for pair in get_config('colors', 'duplications', w)],
     shell:
         """
-        cp {input.colors} {output.colors}
+        cp {input.colors} {output.colors} && \
+        python3 scripts/assign-colors.py \
+            --metadata {input.metadata} \
+            --ordering {input.ordering} \
+            --color-schemes {input.schemes} \
+            --duplications {params.duplications} \
+        >> {output.colors}        
         """
 
 rule export:

diff --git a/config/gisaid.yaml b/config/gisaid.yaml
@@ -157,7 +157,14 @@ traits:
     FALLBACK: true
 
 colors:
-  hardcoded: config/{subtype}/colors_{subtype}.tsv
+  hardcoded: 
+    FALLBACK: config/{subtype}/colors_{subtype}.tsv
+  ordering: 
+    FALLBACK: "config/shared/color_ordering_genoflu.tsv" # for dynamic assignment
+  schemes: 
+    FALLBACK: "config/shared/color_schemes.tsv"
+  duplications:
+    FALLBACK: []
 
 export:
   title:

diff --git a/config/h5n1-cattle-outbreak.yaml b/config/h5n1-cattle-outbreak.yaml
@@ -136,11 +136,15 @@ traits:
     FALLBACK: true
 
 colors:
-  hardcoded: config/h5n1/colors_h5n1.tsv # use H5N1 colors
-  ordering: "config/h5n1-cattle-outbreak/color_ordering.tsv" # for dynamic assignment
-  schemes: "config/shared/color_schemes.tsv"
+  hardcoded: 
+    FALLBACK: config/h5n1/colors_h5n1.tsv # use H5N1 colors
+  ordering: 
+    FALLBACK: "config/h5n1-cattle-outbreak/color_ordering.tsv" # for dynamic assignment
+  schemes: 
+    FALLBACK: "config/shared/color_schemes.tsv"
   duplications:
-    - ["division", "division_metadata"]
+    FALLBACK:
+      - ["division", "division_metadata"]
 
 export:
   genome_title:

diff --git a/config/h5n1-d1.1.yaml b/config/h5n1-d1.1.yaml
@@ -126,12 +126,16 @@ traits:
     FALLBACK: true
 
 colors:
-  hardcoded: config/h5n1/colors_h5n1.tsv # use H5N1 colors
-  ordering: "config/h5n1-cattle-outbreak/color_ordering.tsv" # for dynamic assignment
-  schemes: "config/shared/color_schemes.tsv"
+  hardcoded: 
+    FALLBACK: config/h5n1/colors_h5n1.tsv # use H5N1 colors
+  ordering: 
+    FALLBACK: "config/h5n1-cattle-outbreak/color_ordering.tsv" # for dynamic assignment
+  # NOTE: we could add config/shared/color_ordering_genoflu.tsv here but these builds only have 1 genoflu value
+  schemes: 
+    FALLBACK: "config/shared/color_schemes.tsv"
   duplications:
-    - ["division", "division_metadata"]
-
+    FALLBACK: 
+      - ["division", "division_metadata"]
 
 export:
   genome_title:

diff --git a/config/shared/color_ordering_genoflu.tsv b/config/shared/color_ordering_genoflu.tsv
@@ -0,0 +1,121 @@
+genoflu	A1
+genoflu	A2
+genoflu	A3
+genoflu	A4
+genoflu	A5
+genoflu	A6
+genoflu	B1.1
+genoflu	B1.2
+genoflu	B1.3
+genoflu	B2.1
+genoflu	B2.2
+genoflu	B3.1
+genoflu	B3.10
+genoflu	B3.11
+genoflu	B3.12
+genoflu	B3.13
+genoflu	B3.2
+genoflu	B3.3
+genoflu	B3.4
+genoflu	B3.5
+genoflu	B3.6
+genoflu	B3.7
+genoflu	B3.8
+genoflu	B3.9
+genoflu	B4.1
+genoflu	B5.1
+genoflu	C1.1
+genoflu	C2.1
+genoflu	C3.1
+genoflu	D1.1
+genoflu	D1.2
+genoflu	D1.3
+genoflu	D2.1
+genoflu	Minor01
+genoflu	Minor04
+genoflu	Minor07
+genoflu	Minor08
+genoflu	Minor09
+genoflu	Minor10
+genoflu	Minor11
+genoflu	Minor12
+genoflu	Minor13
+genoflu	Minor14
+genoflu	Minor15
+genoflu	Minor16
+genoflu	Minor17
+genoflu	Minor18
+genoflu	Minor19
+genoflu	Minor24
+genoflu	Minor25
+genoflu	Minor26
+genoflu	Minor27
+genoflu	Minor28
+genoflu	Minor29
+genoflu	Minor30
+genoflu	Minor31
+genoflu	Minor32
+genoflu	Minor33
+genoflu	Minor34
+genoflu	Minor35
+genoflu	Minor36
+genoflu	Minor37
+genoflu	Minor38
+genoflu	Minor39
+genoflu	Minor40
+genoflu	Minor41
+genoflu	Minor42
+genoflu	Minor43
+genoflu	Minor44
+genoflu	Minor45
+genoflu	Minor46
+genoflu	Minor47
+genoflu	Minor48
+genoflu	Minor50
+genoflu	Minor51
+genoflu	Minor52
+genoflu	Minor53
+genoflu	Minor55
+genoflu	Minor56
+genoflu	Minor57
+genoflu	Minor58
+genoflu	Minor60
+genoflu	Minor61
+genoflu	Minor62
+genoflu	Minor63
+genoflu	Minor65
+genoflu	Minor66
+genoflu	Minor67
+genoflu	Minor70
+genoflu	Minor71
+genoflu	Minor73
+genoflu	Minor74
+genoflu	Minor75
+genoflu	Minor76
+genoflu	Minor77
+genoflu	Minor78
+genoflu	Minor79
+genoflu	Minor80
+genoflu	Minor81
+genoflu	Minor82
+genoflu	Minor83
+genoflu	Minor84
+genoflu	Minor86
+genoflu	Minor87
+genoflu	Minor89
+genoflu	Minor90
+genoflu	Minor91
+genoflu	Minor92
+genoflu	Minor93
+genoflu	Minor94
+genoflu	Minor95
+genoflu	Minor97
+genoflu	Minor98
+genoflu	Minor99
+genoflu	Minor100
+genoflu	Minor101
+genoflu	Minor102
+genoflu	Minor103
+genoflu	Minor104
+genoflu	Minor105
+genoflu	Minor106
diff --git a/rules/cattle-flu.smk b/rules/cattle-flu.smk
@@ -162,32 +162,3 @@ rule prune_tree:
             --output-tree {output.tree} \
             --output-metadata {output.node_data}
         """
-
-rule colors_genome:
-    # TODO: add these input files / params to the config YAML. The config YAML must also
-    # define the concept of whether this rule should run so this isn't trivial and is
-    # thus left as a to-do
-    input:
-        metadata = "results/{subtype}/genome/{time}/metadata.tsv", # Always use the genome metadata, even for segment builds
-        ordering = config['colors']['ordering'],
-        schemes = config['colors']['schemes'],
-        colors = config['colors']['hardcoded']
-    output:
-        colors = "results/{subtype}/{segment}/{time}/colors.tsv",
-    params:
-        duplications = ["=".join(pair) for pair in config['colors'].get('duplications', [])]
-    wildcard_constraints:
-        subtype='h5n1-cattle-outbreak|h5n1-d1.1',
-        time="default",
-    shell:
-        """
-        cp {input.colors} {output.colors} && \
-        python3 scripts/assign-colors.py \
-            --metadata {input.metadata} \
-            --ordering {input.ordering} \
-            --color-schemes {input.schemes} \
-            --duplications {params.duplications} \
-        >> {output.colors}        
-        """
-
-ruleorder: colors_genome > colors