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

@@ -13,7 +13,7 @@ rule files:
 files = rules.files.params
 
 rule parse:
-    message: "Parsing provided metadata & sequences into augur formats"
+    """Parsing provided metadata & sequences into augur formats"""
     input:
         metadata = files.input_metadata,
         sequences = files.input_sequences
@@ -34,11 +34,10 @@ rule parse:
         """
 
 rule align:
-    message:
-        """
-        Aligning sequences to {input.reference}
-          - filling gaps with N
-        """
+    """
+    Aligning sequences to {input.reference}
+      - filling gaps with N
+    """
     input:
         sequences = "results/sequences.fasta",
         reference = files.reference
@@ -55,7 +54,7 @@ rule align:
         """
 
 rule tree:
-    message: "Building tree using IQ-TREE"
+    """Building tree using IQ-TREE"""
     input:
         alignment = "results/aligned.fasta"
     output:
@@ -68,11 +67,10 @@ rule tree:
         """
 
 rule refine:
-    message:
-        """
-        Refining tree to add names to internal nodes and inferring a timetree.
-        NOTE: this step can drop samples which are extreme outliers in the root-to-tip analysis
-        """
+    """
+    Refining tree to add names to internal nodes and inferring a timetree.
+    NOTE: this step can drop samples which are extreme outliers in the root-to-tip analysis
+    """
     input:
         tree = "results/tree_raw.nwk",
         alignment = "results/aligned.fasta",
@@ -102,7 +100,7 @@ rule refine:
         """
 
 rule ancestral:
-    message: "Reconstructing ancestral sequences and mutations"
+    """Reconstructing ancestral sequences and mutations"""
     input:
         tree = "results/tree.nwk",
         alignment = "results/aligned.fasta",
@@ -120,7 +118,7 @@ rule ancestral:
         """
 
 rule traits:
-    message: "Inferring ancestral traits for {params.columns!s}"
+    """Inferring ancestral traits for {params.columns!s}"""
     input:
         tree = "results/tree.nwk",
         metadata = "results/metadata.tsv",
@@ -140,7 +138,7 @@ rule traits:
 
 
 rule export:
-    message: "Exporting data files for for auspice"
+    """Exporting data files for for auspice"""
     input:
         tree = "results/tree.nwk",
         metadata = "results/metadata.tsv",
@@ -166,7 +164,7 @@ rule export:
         """
 
 rule clean:
-    message: "Removing directories: {params}"
+    """Removing directories: {params}"""
     params:
         "results ",
         "auspice"