chore: replace snakemake message directives with comments

This is a stylistic change to make the Snakemake code conform to documented
Nextstrain Snakemake Styleguide:

  Avoid the message rule attribute.
  When the message attribute is defined, Snakemake suppresses other
  critical details that otherwise get displayed by default (e.g., job id,
  rule name, input, output, etc.).

Snakefile

@@ -14,7 +14,7 @@ rule files:
 files = rules.files.params
 
 rule download:
-    message: "Downloading sequences and metadata from data.nextstrain.org"
+    """Downloading sequences and metadata from data.nextstrain.org"""
     output:
         sequences = "data/sequences.fasta.zst",
         metadata = "data/metadata.tsv.zst"
@@ -28,7 +28,7 @@ rule download:
         """
 
 rule decompress:
-    message: "Decompressing sequences and metadata"
+    """Decompressing sequences and metadata"""
     input:
         sequences = "data/sequences.fasta.zst",
         metadata = "data/metadata.tsv.zst"
@@ -42,14 +42,13 @@ rule decompress:
         """
 
 rule filter:
-    message:
-        """
-        Filtering to
-          - {params.sequences_per_group} sequence(s) per {params.group_by!s}
-          - from {params.min_date} onwards
-          - excluding strains in {input.exclude}
-          - minimum genome length of {params.min_length} (50% of Zika virus genome)
-        """
+    """
+    Filtering to
+      - {params.sequences_per_group} sequence(s) per {params.group_by!s}
+      - from {params.min_date} onwards
+      - excluding strains in {input.exclude}
+      - minimum genome length of {params.min_length} (50% of Zika virus genome)
+    """
     input:
         sequences = "data/sequences.fasta",
         metadata = "data/metadata.tsv",
@@ -75,11 +74,10 @@ rule filter:
         """
 
 rule align:
-    message:
-        """
-        Aligning sequences to {input.reference}
-          - filling gaps with N
-        """
+    """
+    Aligning sequences to {input.reference}
+      - filling gaps with N
+    """
     input:
         sequences = "results/filtered.fasta",
         reference = files.reference
@@ -96,7 +94,7 @@ rule align:
         """
 
 rule tree:
-    message: "Building tree"
+    """Building tree"""
     input:
         alignment = "results/aligned.fasta"
     output:
@@ -109,14 +107,13 @@ rule tree:
         """
 
 rule refine:
-    message:
-        """
-        Refining tree
-          - estimate timetree
-          - use {params.coalescent} coalescent timescale
-          - estimate {params.date_inference} node dates
-          - filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
-        """
+    """
+    Refining tree
+      - estimate timetree
+      - use {params.coalescent} coalescent timescale
+      - estimate {params.date_inference} node dates
+      - filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
+    """
     input:
         tree = "results/tree_raw.nwk",
         alignment = "results/aligned.fasta",
@@ -144,7 +141,7 @@ rule refine:
         """
 
 rule ancestral:
-    message: "Reconstructing ancestral sequences and mutations"
+    """Reconstructing ancestral sequences and mutations"""
     input:
         tree = "results/tree.nwk",
         alignment = "results/aligned.fasta"
@@ -162,7 +159,7 @@ rule ancestral:
         """
 
 rule translate:
-    message: "Translating amino acid sequences"
+    """Translating amino acid sequences"""
     input:
         tree = "results/tree.nwk",
         node_data = "results/nt_muts.json",
@@ -179,11 +176,10 @@ rule translate:
         """
 
 rule traits:
-    message:
-        """
-        Inferring ancestral traits for {params.columns!s}
-          - increase uncertainty of reconstruction by {params.sampling_bias_correction} to partially account for sampling bias
-        """
+    """
+    Inferring ancestral traits for {params.columns!s}
+      - increase uncertainty of reconstruction by {params.sampling_bias_correction} to partially account for sampling bias
+    """
     input:
         tree = "results/tree.nwk",
         metadata = "data/metadata.tsv"
@@ -204,7 +200,7 @@ rule traits:
         """
 
 rule export:
-    message: "Exporting data files for for auspice"
+    """Exporting data files for for auspice"""
     input:
         tree = "results/tree.nwk",
         metadata = "data/metadata.tsv",
@@ -231,7 +227,7 @@ rule export:
         """
 
 rule clean:
-    message: "Removing directories: {params}"
+    """Removing directories: {params}"""
     params:
         "data ",
         "results ",