From 5c06dd6a3273057144a8d5e1305c7cbdfc329b66 Mon Sep 17 00:00:00 2001
From: Johannes Koester <johannes.koester@uni-due.de>
Date: Mon, 5 Feb 2024 08:21:19 +0100
Subject: [PATCH] fix: fixed bug in handling of resource overrides for remote
 job submission

---
 snakemake/cli.py        | 11 +++++++----
 snakemake/settings.py   |  4 ++--
 snakemake/spawn_jobs.py |  9 ++++++++-
 3 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/snakemake/cli.py b/snakemake/cli.py
index 3a567656d..3d8f1821d 100644
--- a/snakemake/cli.py
+++ b/snakemake/cli.py
@@ -31,6 +31,7 @@
     ResourceScopesException,
     print_exception,
 )
+from snakemake.io import flag
 from snakemake.resources import (
     DefaultResources,
     ResourceScopes,
@@ -81,18 +82,20 @@ def parse_set_resources(args):
     assignments = defaultdict(dict)
     if args is not None:
         for entry in args:
-            key, value = parse_key_value_arg(entry, errmsg=errmsg, strip_quotes=False)
+            key, orig_value = parse_key_value_arg(
+                entry, errmsg=errmsg, strip_quotes=False
+            )
             key = key.split(":")
             if len(key) != 2:
                 raise ValueError(errmsg)
             rule, resource = key
             try:
-                value = int(value)
+                value = int(orig_value)
             except ValueError:
-                value = eval_resource_expression(value)
+                value = eval_resource_expression(orig_value)
             if isinstance(value, int) and value < 0:
                 raise ValueError(errmsg)
-            assignments[rule][resource] = value
+            assignments[rule][resource] = flag(value, "orig_arg", orig_value)
     return assignments
 
 
diff --git a/snakemake/settings.py b/snakemake/settings.py
index 44924a571..69a7e8476 100644
--- a/snakemake/settings.py
+++ b/snakemake/settings.py
@@ -1,7 +1,7 @@
 from abc import ABC
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Optional
+from typing import Any, Optional
 from typing import Mapping, Sequence, Set
 
 import immutables
@@ -281,7 +281,7 @@ class ResourceSettings(SettingsBase):
     overwrite_threads: Mapping[str, int] = immutables.Map()
     overwrite_scatter: Mapping[str, int] = immutables.Map()
     overwrite_resource_scopes: Mapping[str, str] = immutables.Map()
-    overwrite_resources: Mapping[str, Mapping[str, int]] = immutables.Map()
+    overwrite_resources: Mapping[str, Mapping[str, Any]] = immutables.Map()
     default_resources: Optional[DefaultResources] = None
 
     def __post_init__(self):
diff --git a/snakemake/spawn_jobs.py b/snakemake/spawn_jobs.py
index 2dbbc1013..9231d7d92 100644
--- a/snakemake/spawn_jobs.py
+++ b/snakemake/spawn_jobs.py
@@ -7,6 +7,7 @@
 from snakemake_interface_storage_plugins.registry import StoragePluginRegistry
 
 from snakemake import common
+from snakemake.io import get_flag_value, is_flagged
 from snakemake.settings import SharedFSUsage
 
 if TYPE_CHECKING:
@@ -82,10 +83,16 @@ def get_storage_provider_envvars(self):
         }
 
     def get_set_resources_args(self):
+        def get_orig_arg(value):
+            if is_flagged(value, "orig_arg"):
+                return get_flag_value(value, "orig_arg")
+            else:
+                return value
+
         return format_cli_arg(
             "--set-resources",
             [
-                f"{rule}:{name}={value}"
+                f"{rule}:{name}={get_orig_arg(value)}"
                 for rule, res in self.workflow.resource_settings.overwrite_resources.items()
                 for name, value in res.items()
             ],