run: support registered workflow Snakefile and configfile

Allow maintainers to define paths to each workflow's Snakefile and configfile 
in the nextstrain-pathogen.yaml. Using mpox as an example, this allows the named 
workflows to use the shared Snakefile and their own custom configfiles without 
needing to create separate Snakefiles for each workflow.
```
---
compatibility:
  nextstrain run:
    ingest: ~
    phylogenetic/all-clades:
        snakefile: phylogenetic/Snakefile
        configfile: phylogenetic/defaults/mpxv/config.yaml
    phylogenetic/clade-I:
        snakefile: phylogenetic/Snakefile
        configfile: phylogenetic/defaults/clade-i/config.yaml
    phylogenetic/clade-IIb:
        snakefile: phylogenetic/Snakefile
        configfile: phylogenetic/defaults/hmpxv1/config.yaml
    phylogenetic/lineage-B.1:
        snakefile: phylogenetic/Snakefile
        configfile: phylogenetic/deafults/hmpxv1_big/config.yaml
```

Author: joverlee521

nextstrain/cli/command/run.py

@@ -231,27 +231,42 @@ def run(opts):
     if opts.workflow not in pathogen.registered_workflows():
         print(f"The {opts.workflow!r} workflow is not registered as a compatible workflow, but trying to run anyways.")
 
-    workflow_directory = pathogen.workflow_path(opts.workflow)
+    workflow_files = pathogen.workflow_files(opts.workflow)
+    workflow_snakefile = workflow_files["snakefile"]
 
-    if not workflow_directory.is_dir() or not (workflow_directory / "Snakefile").is_file():
+    if not workflow_snakefile.is_file():
         raise UserError(f"""
-            No {opts.workflow!r} workflow for pathogen {opts.pathogen!r} found {f"in {str(workflow_directory)!r}" if DEBUGGING else "locally"}.
+            No {opts.workflow!r} workflow for pathogen {opts.pathogen!r} found {f"(Snakefile {workflow_snakefile!r} does not exist)" if DEBUGGING else "locally"}.
 
             Maybe you need to update to a newer version of the pathogen?
 
             Hint: to update the pathogen, run `nextstrain update {shquote(pathogen.name)}`.
             """)
 
+    if workflow_configfile := workflow_files["configfile"]:
+        assert workflow_configfile.is_file(), \
+            f"Workflow's registered config file {workflow_configfile!r} does not exist."
+
     # The pathogen volume is the pathogen directory (i.e. repo).
-    # The workflow volume is the workflow directory within the pathogen directory.
     # The build volume is the user's analysis directory and will be the working directory.
-    pathogen_volume, workflow_volume = build.pathogen_volumes(workflow_directory, name = "pathogen")
+    pathogen_volume, _ = build.pathogen_volumes(pathogen.path, name = "pathogen")
     build_volume = NamedVolume("build", opts.analysis_directory)
 
     # for containerized runtimes (e.g. Docker, Singularity, and AWS Batch)
     opts.volumes.append(pathogen_volume)
     opts.volumes.append(build_volume)
 
+    # Resolve paths for workflow files
+    resolved_pathogen = (
+        docker.mount_point(pathogen_volume)
+            if opts.__runner__ in {docker, singularity, aws_batch} else
+        pathogen_volume.src.resolve(strict = True)
+    )
+    resolved_snakefile = resolved_pathogen / workflow_snakefile.relative_to(pathogen.path)
+    resolved_configfile = None
+    if workflow_configfile:
+        resolved_configfile = resolved_pathogen / workflow_configfile.relative_to(pathogen.path)
+
     print(f"Running the {opts.workflow!r} workflow for pathogen {pathogen}")
 
     # Set up Snakemake invocation.
@@ -276,10 +291,10 @@ def run(opts):
 
         # Workdir will be the analysis volume (/nextstrain/build in a
         # containerized runtime), so explicitly point to the Snakefile.
-        "--snakefile=%s/Snakefile" % (
-            docker.mount_point(workflow_volume)
-                if opts.__runner__ in {docker, singularity, aws_batch} else
-            workflow_volume.src.resolve(strict = True)),
+        "--snakefile=%s" % (resolved_snakefile),
+
+        *(["--configfile=%s" % (resolved_configfile)]
+            if resolved_configfile else []),
 
         # Pass thru appropriate resource options.
         #

nextstrain/cli/pathogens.py

@@ -326,6 +326,26 @@ def workflow_path(self, workflow: str) -> Path:
         return self.path / workflow
 
 
+    def workflow_files(self, workflow: str) -> Dict:
+        """
+        Parses :attr:`.registration` to get the path to a *workflow* files,
+        snakefile and configfile.
+        """
+        files = {
+            "snakefile": self.workflow_path(workflow) / "Snakefile",
+            "configfile": None,
+        }
+
+        if workflow_registration := self.registered_workflows().get(workflow):
+            if snakefile := workflow_registration.get("snakefile"):
+                files["snakefile"] = self.path / snakefile
+
+            if configfile := workflow_registration.get("configfile"):
+                files["configfile"] = self.path / configfile
+
+        return files
+
+
     def setup(self, dry_run: bool = False, force: bool = False) -> SetupStatus:
         """
         Downloads and installs this pathogen version from :attr:`.url`.