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

CHANGES.md

@@ -24,6 +24,11 @@ development source code and as such may not be routinely kept up to date.
 
   ([#501](https://github.com/nextstrain/cli/pull/501))
 
+* `nextstrain build` and `nextstrain run` now run Snakemake with the
+  `--benchmark-extended` option for more detailed benchmark files when used with
+  recent versions of managed runtimes.
+  ([#467](https://github.com/nextstrain/cli/issues/467))
+
 # 10.4.2 (7 January 2026)
 
 ## Improvements

doc/changes.md

@@ -28,6 +28,11 @@ development source code and as such may not be routinely kept up to date.
 
   ([#501](https://github.com/nextstrain/cli/pull/501))
 
+* `nextstrain build` and `nextstrain run` now run Snakemake with the
+  `--benchmark-extended` option for more detailed benchmark files when used with
+  recent versions of managed runtimes.
+  ([#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 docker, conda, 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]
@@ -443,6 +452,23 @@ def pathogen_volumes(directory: Path, *, name = "build") -> Tuple[NamedVolume, N
     return build_volume, working_volume
 
 
+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__ in (docker, aws_batch, singularity):
+        image = runner.configured_image(opts)
+        if opts.__runner__ is singularity:
+            image = singularity.docker_image_name(image)
+        return docker.image_supports(docker.IMAGE_FEATURE.benchmark_extended, image)
+
+    if opts.__runner__ is conda:
+        return conda.env_supports(conda.ENV_FEATURE.benchmark_extended)
+
+    return False
+
+
 def parse_snakemake_args(args):
     """
     Inspects a tiny subset of Snakemake's CLI arguments in order to determine

nextstrain/cli/command/run.py

@@ -292,6 +292,10 @@ def run(opts):
         # Useful to see what's going on; see also 08ffc925.
         "--printshellcmds",
 
+        # Useful to have additional information in benchmark files.
+        *(["--benchmark-extended"]
+            if build.supports_benchmark_extended(opts) else []),
+
         # 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/__init__.py

@@ -239,10 +239,7 @@ def run(opts: Options, working_volume: NamedVolume = None, extra_env: Env = {},
             supports these runtimes with `nextstrain check-setup`.
             """)
 
-    # Account for potentially different defaults for --image depending on the
-    # selected runner.
-    if opts.__runner__ is singularity and opts.image is docker.DEFAULT_IMAGE:
-        opts.image = singularity.DEFAULT_IMAGE
+    opts.image = configured_image(opts)
 
     if envdirs := os.environ.get("NEXTSTRAIN_RUNTIME_ENVDIRS"):
         try:
@@ -277,3 +274,15 @@ def replace_ellipsis(items, elided_items):
         y for x in items
           for y in (elided_items if x is ... else [x])
     ]
+
+
+def configured_image(opts: Options) -> str:
+    """
+    Return the effective image for the selected runner.
+    """
+    # Account for potentially different defaults for --image depending on the
+    # selected runner.
+    if opts.__runner__ is singularity and opts.image is docker.DEFAULT_IMAGE:
+        return singularity.DEFAULT_IMAGE
+
+    return opts.image

nextstrain/cli/runner/conda.py

@@ -106,6 +106,7 @@
 import sys
 import tarfile
 import traceback
+from enum import Enum
 from pathlib import Path, PurePosixPath
 from tempfile import TemporaryFile
 from typing import IO, Iterable, List, NamedTuple, Optional, cast
@@ -173,6 +174,27 @@
 }
 
 
+class ENV_FEATURE(Enum):
+    # --benchmark-extended was introduced in Snakemake 8.11.0.
+    benchmark_extended = "20250717T164942Z"
+
+
+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 +116,9 @@ class IMAGE_FEATURE(Enum):
     # file overwriting) in ZIP extraction.
     aws_batch_overlays = "build-20250321T184358Z"
 
+    # --benchmark-extended was introduced in Snakemake 8.11.0.
+    benchmark_extended = "build-20250717T164950Z"
+
 
 def register_arguments(parser) -> None:
     # Docker development options

nextstrain/cli/util.py

@@ -64,6 +64,7 @@ def colored(color, text):
     )
 
 
+# TODO: Use str.removeprefix/removesuffix once Python 3.9 is the minimum supported version.
 def remove_prefix(prefix, string):
     return re.sub('^' + re.escape(prefix), '', string)