build, run: Always run Snakemake with --benchmark-extended

CHANGES.md

@@ -24,6 +24,10 @@ development source code and as such may not be routinely kept up to date.
 
   ([#501](https://github.com/nextstrain/cli/pull/501))
 
+* The `build` and `run` commands now run `snakemake` with the
+  `--benchmark-extended` option for more detailed benchmark files.
+  ([#467](https://github.com/nextstrain/cli/issues/467))
+
 # 10.4.2 (7 January 2026)
 
 ## Improvements

doc/changes.md

@@ -28,6 +28,10 @@ development source code and as such may not be routinely kept up to date.
 
   ([#501](https://github.com/nextstrain/cli/pull/501))
 
+* The `build` and `run` commands now run `snakemake` with the
+  `--benchmark-extended` option for more detailed benchmark files.
+  ([#467](https://github.com/nextstrain/cli/issues/467))
+
 (v10-4-2)=
 ## 10.4.2 (7 January 2026)
 

nextstrain/cli/command/build.py

@@ -24,7 +24,7 @@
 from ..argparse import add_extended_help_flags, AppendOverwriteDefault, SKIP_AUTO_DEFAULT_IN_HELP
 from ..debug import debug
 from ..errors import UsageError, UserError
-from ..runner import docker, singularity, aws_batch
+from ..runner import conda, docker, singularity, aws_batch
 from ..util import byte_quantity, runner_name, split_image_name, warn
 from ..volume import NamedVolume
 
@@ -206,7 +206,7 @@ def register_parser(subparser):
         nargs   = "?")
 
     # Register runner flags and arguments
-    runner.register_runners(parser, exec = ["snakemake", "--printshellcmds", ...])
+    runner.register_runners(parser, exec = ["snakemake", ...])
 
     return parser
 
@@ -243,12 +243,21 @@ def run(opts):
         opts.volumes.append(build_volume) # for Docker, Singularity, and AWS Batch
 
 
-    # Automatically pass thru appropriate resource options to Snakemake to
-    # avoid the user having to repeat themselves (once for us, once for
-    # snakemake).
     if opts.exec == "snakemake":
+        opts.default_exec_args += [
+            # Useful to see what's going on; see also 08ffc925.
+            "--printshellcmds",
+
+            # Useful to have additional information in benchmark files.
+            *(["--benchmark-extended"]
+                if supports_benchmark_extended(opts) else []),
+        ]
+
         snakemake_opts = parse_snakemake_args(opts.extra_exec_args)
 
+        # Automatically pass thru appropriate resource options to Snakemake to
+        # avoid the user having to repeat themselves (once for us, once for
+        # snakemake).
         if not snakemake_opts["--cores"]:
             if opts.cpus:
                 opts.extra_exec_args += ["--cores=%d" % opts.cpus]
@@ -308,6 +317,22 @@ def run(opts):
     return runner.run(opts, working_volume = working_volume, cpus = opts.cpus, memory = opts.memory)
 
 
+def supports_benchmark_extended(opts) -> bool:
+    """
+    Check if the runner's image or environment supports Snakemake's
+    ``--benchmark-extended`` option (requires Snakemake ≥8.11.0).
+    """
+    if opts.__runner__ is docker:
+        return docker.image_supports(docker.IMAGE_FEATURE.benchmark_extended, opts.image)
+    if opts.__runner__ is aws_batch:
+        return docker.image_supports(docker.IMAGE_FEATURE.benchmark_extended, opts.image)
+    if opts.__runner__ is singularity:
+        return docker.image_supports(docker.IMAGE_FEATURE.benchmark_extended, opts.image.removeprefix("docker://"))
+    if opts.__runner__ is conda:
+        return conda.env_supports(conda.ENV_FEATURE.benchmark_extended)
+    return False
+
+
 def assert_overlay_volumes_support(opts):
     """
     Check that runtime overlays are supported, if given.

nextstrain/cli/command/run.py

@@ -292,6 +292,9 @@ def run(opts):
         # Useful to see what's going on; see also 08ffc925.
         "--printshellcmds",
 
+        # Useful to have additional information in benchmark files.
+        "--benchmark-extended",
+
         # In our experience,¹ it's rarely useful to fail on incomplete outputs
         # (Snakemake's default behaviour) instead of automatically regenerating
         # them.

nextstrain/cli/runner/conda.py

@@ -98,6 +98,7 @@
     usable for the platform.
 """
 
+from enum import Enum
 import json
 import os
 import platform
@@ -173,6 +174,28 @@
 }
 
 
+class ENV_FEATURE(Enum):
+    # --benchmark-extended was introduced in Snakemake 8.11.0.
+    # FIXME: find the earliest supported image
+    benchmark_extended = "20251126T221614Z"
+
+
+def env_supports(feature: ENV_FEATURE) -> bool:
+    """
+    Test if the conda environment supports a *feature*, i.e. by version
+    comparison of the nextstrain-base package against the feature's first
+    release.
+
+    If the nextstrain-base package is not found, it is assumed to not have
+    support for the feature.
+    """
+    meta = package_meta(NEXTSTRAIN_BASE)
+    if not meta:
+        return False
+    version = meta.get("version", "0")
+    return parse_version_lax(version) >= parse_version_lax(feature.value)
+
+
 def register_arguments(parser) -> None:
     """
     No-op.  No arguments necessary.

nextstrain/cli/runner/docker.py

@@ -116,6 +116,10 @@ class IMAGE_FEATURE(Enum):
     # file overwriting) in ZIP extraction.
     aws_batch_overlays = "build-20250321T184358Z"
 
+    # --benchmark-extended was introduced in Snakemake 8.11.0.
+    # FIXME: find the earliest supported image
+    benchmark_extended = "build-20260310T234712Z"
+
 
 def register_arguments(parser) -> None:
     # Docker development options