diff --git a/schemas/settings.yaml b/schemas/settings.yaml
index 1009885ff..8e333c352 100644
--- a/schemas/settings.yaml
+++ b/schemas/settings.yaml
@@ -26,6 +26,10 @@ properties:
     notes: |
       This includes raw values such as commodity balance duals, which may be useful for debugging
       the model or understanding results in more detail.
+  copy_input_files:
+    type: boolean
+    description: Whether to copy input files to the output folder
+    default: true
   results_root:
     type: string
     description: Results root path to save MUSE2 results
diff --git a/src/cli.rs b/src/cli.rs
index c32c2da01..c38491ace 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -39,6 +39,10 @@ pub struct RunOpts {
     /// Whether to write additional information to CSV files
     #[arg(long)]
     pub debug_model: bool,
+
+    /// Whether to skip copying input files to the output folder
+    #[arg(long)]
+    pub no_copy_input_files: bool,
 }
 
 /// Options for the `graph` command
@@ -134,6 +138,9 @@ pub fn handle_run_command(model_path: &Path, opts: &RunOpts) -> Result<()> {
     if opts.overwrite {
         settings.overwrite = true;
     }
+    if opts.no_copy_input_files {
+        settings.copy_input_files = false;
+    }
 
     // Get path to output folder
     let pathbuf: PathBuf;
@@ -161,9 +168,10 @@ pub fn handle_run_command(model_path: &Path, opts: &RunOpts) -> Result<()> {
         .to_str()
         .context("Invalid chars in model directory name")?;
 
-    copy_input_files(&model_path, output_path, model_name)
-        .context("Failed to copy input files to output directory.")?;
-
+    if settings.copy_input_files {
+        copy_input_files(&model_path, output_path, model_name)
+            .context("Failed to copy input files to output directory.")?;
+    }
     // Initialise program logger
     log::init(&settings.log_level, Some(output_path)).context("Failed to initialise logging.")?;
 
diff --git a/src/settings.rs b/src/settings.rs
index 7403a1b3b..6697b9416 100644
--- a/src/settings.rs
+++ b/src/settings.rs
@@ -52,6 +52,8 @@ pub struct Settings {
     pub results_root: PathBuf,
     /// Results root path to save MUSE2 graph outputs. Defaults to `muse2_graphs`.
     pub graph_results_root: PathBuf,
+    /// Whether to copy input files to the output folder.
+    pub copy_input_files: bool,
 }
 
 impl Default for Settings {
@@ -62,6 +64,7 @@ impl Default for Settings {
             debug_model: false,
             results_root: PathBuf::from("muse2_results"),
             graph_results_root: PathBuf::from("muse2_graphs"),
+            copy_input_files: true,
         }
     }
 }
diff --git a/tests/regenerate_test_data.sh b/tests/regenerate_test_data.sh
old mode 100755
new mode 100644
index 97ca78784..e65426642
--- a/tests/regenerate_test_data.sh
+++ b/tests/regenerate_test_data.sh
@@ -26,6 +26,9 @@ run_example() {
     env MUSE2_LOG_LEVEL=error MUSE2_USE_DEFAULT_SETTINGS=1 \
         cargo -q run example run -o "data/$example" "$example" \
             --overwrite $@
+    env MUSE2_LOG_LEVEL=error MUSE2_USE_DEFAULT_SETTINGS=1 \
+        cargo -q run example run -o "data/${example}_debug" "$example" \
+            --overwrite --no-copy-input-files $@
 }
 
 for example in $examples; do