impose wildcard constraint on nextclade_dataset

workflow/Snakefile

@@ -189,12 +189,15 @@ rule nextclade_dataset:
   Download Nextclade dataset.
   """
   message: "{wildcards.dataset} | Downloading Nextclade sars-cov-2 dataset."
+  wildcard_constraints:
+    # The tag will always begin with the year (ex. 2022)
+    tag="([0-9]){4}.*",
   output:
     dataset_dir = directory("data/{dataset}_{tag}"),
   benchmark:
     "benchmarks/{rule}/{{dataset}}_{{tag}}_{today}.tsv".format(today=today, rule=rule_name),
   log:
-    "logs/{rule}/{{dataset}}_{{tag}}_{today}.txt".format(today=today, rule=rule_name),
+    "logs/{rule}/{{dataset}}_{{tag}}_{today}.log".format(today=today, rule=rule_name),
   shell:
     """
     nextclade dataset get --name {wildcards.dataset} --tag {wildcards.tag} --output-dir {output.dataset_dir} > {log} 2>&1;
@@ -571,36 +574,6 @@ rule usher_subtree:
     python3 scripts/usher_collapse.py --indir {output.subtrees_dir} --outdir {output.collapse_dir} >> {log} 2>&1;
     """
 
-# -----------------------------------------------------------------------------
-rule_name = "usher_plot"
-rule usher_plot:
-  """
-  Plot UShER subtrees.
-  """
-  message: "{wildcards.build} | Plotting UShER subtrees."
-  input:
-    collapse_dir = rules.usher_subtree.output.collapse_dir,
-    samples      = "results/{build}/sc2rf.recombinants.txt",
-  output:
-    plot_dir = report(
-                directory("results/{build}/subtrees_plot"),
-                patterns=["{name}.png"],
-                caption="report/usher.rst",
-                category="Stage 3: UShER",
-                labels={"build": "{build}", "description" : "{name} Image"},
-              ),
-  benchmark:
-    "benchmarks/{rule}/{{build}}_{today}.tsv".format(today=today, rule=rule_name),
-  log:
-    "logs/{rule}/{{build}}_{today}.log".format(today=today, rule=rule_name),
-  shell:
-    """
-    mkdir -p {output.plot_dir};
-    for subtree in $(ls {input.collapse_dir}/*.nwk); do
-      python3 scripts/usher_plot.py --tree $subtree --strains {input.samples} --outdir {output.plot_dir};
-    done > {log} 2>&1;
-    """
-
 # -----------------------------------------------------------------------------#
 #  STAGE 4: Summary
 # -----------------------------------------------------------------------------#