build: Run Snakemake with --rerun-incomplete

CHANGES.md

@@ -13,6 +13,11 @@ development source code and as such may not be routinely kept up to date.
 
 # __NEXT__
 
+## Improvements
+
+* `nextstrain build` now runs Snakemake with the `--rerun-incomplete` option,
+  aligning with `nextstrain run`.
+  ([#515](https://github.com/nextstrain/cli/pull/515))
 
 # 10.5.0 (25 March 2026)
 

doc/changes.md

@@ -16,6 +16,12 @@ development source code and as such may not be routinely kept up to date.
 (v-next)=
 ## __NEXT__
 
+(v-next-improvements)=
+### Improvements
+
+* `nextstrain build` now runs Snakemake with the `--rerun-incomplete` option,
+  aligning with `nextstrain run`.
+  ([#515](https://github.com/nextstrain/cli/pull/515))
 
 (v10-5-0)=
 ## 10.5.0 (25 March 2026)

nextstrain/cli/command/build.py

@@ -251,6 +251,13 @@ def run(opts):
             # Useful to have additional information in benchmark files.
             *(["--benchmark-extended"]
                 if 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.
+            #
+            # ¹ <https://discussion.nextstrain.org/t/snakemake-throwing-incompletefilesexception-when-using-forceall/1397/4>
+            "--rerun-incomplete",
         ]
 
         snakemake_opts = parse_snakemake_args(opts.extra_exec_args)