feat: implement solution for #58

torchbase/cli.py

@@ -172,12 +172,32 @@ def compress_stream(file_obj):
 # Main running method
 #
 
+def _strategy_callback(ctx, param, value):
+    """Callback to mark when strategy is explicitly set."""
+    ctx.ensure_object(dict)
+    # Check if the parameter came from user input (not default)
+    if hasattr(ctx, 'get_parameter_source'):
+        source = ctx.get_parameter_source(param.name)
+        if source and source.name == 'COMMANDLINE':
+            ctx.obj['_strategy_explicit'] = True
+    return value
+
+
 @cli.command("run", context_settings=dict(ignore_unknown_options=True, allow_extra_args=True))
 @click.option("--cromwell-opts", "cromwell_options", nargs=1, default="", type=click.STRING)
 @torch
 @click.option("-m", "--method", nargs=1, default="main", type=click.STRING)
 @click.option("--workflow", default=None, help="Override workflow torch (namespace/name format)")
 @click.option("-o", "--output", default=None, help="Output file for results")
+@click.option(
+    "--strategy",
+    type=click.Choice(['fast', 'balanced', 'sensitive']),
+    default='balanced',
+    callback=_strategy_callback,
+    is_eager=True,
+    help="Typing strategy (default=balanced): fast (MinHash only), "
+    "balanced (MinHash+alignment), sensitive (full alignment). "
+    "Cannot be used with embedded workflows.")
 @ReadsParam("-c", "--contigs")
 @ReadsParam("-r", "--reads")
 @ReadsParam("-pe1", "--paired1", "--pe1")
@@ -186,7 +206,7 @@ def compress_stream(file_obj):
 @ReadsParam("-l", "--longreads")
 @click.argument('torch_args', nargs=-1, type=click.UNPROCESSED)
 @click.pass_context
-def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=None, contigs=None, reads=None, paired1=None, paired2=None, interlaced=None, longreads=None, torch_args=[]):
+def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=None, strategy='balanced', contigs=None, reads=None, paired1=None, paired2=None, interlaced=None, longreads=None, torch_args=[]):
     "Run the selected torch."
     from torchbase.torchfs import Torch
     from torchbase.registry import RegistryManager
@@ -203,8 +223,18 @@ def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=N
         # Load data torch
         data_torch = Torch.load(torch)
 
-        # Determine workflow to use
-        workflow_torch = data_torch
+        # Check for conflict: --strategy cannot be used with embedded workflows
+        # Check if user explicitly specified --strategy via the callback flag
+        user_specified_strategy = clx.obj.get('_strategy_explicit', False) if clx.obj else False
+
+        if user_specified_strategy and data_torch.workflow:
+            raise click.ClickException(
+                "Cannot use --strategy with torch-embedded workflows. "
+                "The torch already has a custom workflow (main.wdl) defined."
+            )
+
+        # Determine workflow file to use
+        workflow_file = None
 
         if workflow:
             # User specified custom workflow
@@ -213,31 +243,57 @@ def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=N
             try:
                 workflow_path = manager.fetch_torch(workflow)
                 workflow_torch = Torch.load(workflow_path)
+                workflow_file = workflow_torch.workflow
             except Exception as e:
                 raise click.ClickException(f"Failed to fetch workflow {workflow}: {str(e)}")
-        elif not data_torch.workflow:
-            # No workflow in data torch, try default
+        elif data_torch.workflow:
+            # Torch has embedded workflow
+            workflow_file = data_torch.workflow
+        elif user_specified_strategy:
+            # User explicitly specified --strategy, use built-in workflow
+            strategy_to_workflow = {
+                'fast': 'fast_typing.wdl',
+                'balanced': 'balanced_typing.wdl',
+                'sensitive': 'sensitive_typing.wdl',
+            }
+            workflow_filename = strategy_to_workflow.get(strategy)
+            if not workflow_filename:
+                raise click.ClickException(f"Unknown strategy: {strategy}")
+
+            # Resolve workflow path relative to torchbase package
+            import torchbase
+            torchbase_dir = Path(torchbase.__file__).parent
+            builtin_workflow = torchbase_dir / 'workflows' / 'builtin' / workflow_filename
+
+            if not builtin_workflow.exists():
+                raise click.ClickException(
+                    f"Built-in workflow not found: {builtin_workflow}"
+                )
+
+            workflow_file = builtin_workflow
+        else:
+            # No --strategy specified and torch has no workflow
+            # Try default workflow for backward compatibility
             try:
                 config = RegistryConfig.load()
                 manager = RegistryManager(config)
                 default_workflow_path = manager.fetch_torch("torchbase/default-workflow")
                 workflow_torch = Torch.load(default_workflow_path)
+                workflow_file = workflow_torch.workflow
             except Exception as e:
                 raise click.ClickException(
                     f"Workflow not found in torch and default workflow fetch failed: {str(e)}"
                 )
 
-        # Validate workflow exists and is named main.wdl
-        if not workflow_torch.workflow:
-            raise click.ClickException("No workflow found (main.wdl) in torch")
+        # Validate workflow exists
+        if not workflow_file:
+            raise click.ClickException("No workflow found")
 
-        if workflow_torch.workflow.name != "main.wdl":
-            raise click.ClickException(
-                f"Workflow must be named 'main.wdl', found: {workflow_torch.workflow.name}"
-            )
+        if isinstance(workflow_file, str):
+            workflow_file = Path(workflow_file)
 
         # Build miniwdl command
-        miniwdl_cmd = ['miniwdl', 'run', str(workflow_torch.workflow)]
+        miniwdl_cmd = ['miniwdl', 'run', str(workflow_file)]
 
         # Add input files
         if contigs: