diff --git a/metatlas/untargeted/run_untargeted_pipeline.py b/metatlas/untargeted/run_untargeted_pipeline.py
index 9b81e820..ab99d2d4 100644
--- a/metatlas/untargeted/run_untargeted_pipeline.py
+++ b/metatlas/untargeted/run_untargeted_pipeline.py
@@ -46,7 +46,7 @@ def main():
 
     ##### Step 5/7: Submitting new FBMN jobs to GNPS2
     mzm.submit_fbmn_jobs(output_dir=args.output_dir, overwrite_fbmn=args.overwrite_fbmn, direct_input=args.direct_input, skip_fbmn_submit=step_bools[4], \
-                        raw_data_dir=args.raw_data_dir,raw_data_subdir=args.raw_data_subdir)
+                        mirror_raw_data=args.mirror_raw_data, mirror_mzmine_results=args.mirror_mzmine_results, raw_data_dir=args.raw_data_dir,raw_data_subdir=args.raw_data_subdir)
 
     ##### Step 6/7: Checking for completed FBMN jobs and downloading results
     mzm.download_fbmn_results(output_dir=args.output_dir, overwrite_fbmn=args.overwrite_fbmn,direct_input=args.direct_input, \
@@ -82,6 +82,9 @@ def add_arguments(parser):
     parser.add_argument('--nonpolar_solvent_front', type=float, default=0.5, help='Retention time to use as C18/LIPID solvent front (mins) for filtering features')
     ## Step 3 only
     parser.add_argument('--overwrite_mzmine', type=bool, default=False, help='Overwrite existing mzmine results files that are already in the output directory')
+    ## Step 5 only
+    parser.add_argument('--mirror_raw_data', type=bool, default=True, help='Mirror raw data files to GNPS2')
+    parser.add_argument('--mirror_mzmine_results', type=bool, default=True, help='Mirror mzmine results files to GNPS2')
     ## Step 7 only
     parser.add_argument('--download_dir', type=str, default='/global/cfs/cdirs/metatlas/projects/untargeted_outputs', help='Path to the download folder')
     parser.add_argument('--overwrite_zip',type=bool, default=False, help='Overwrite existing zip files in download folder')
diff --git a/metatlas/untargeted/tools.py b/metatlas/untargeted/tools.py
index 1f37cbcf..7132120e 100644
--- a/metatlas/untargeted/tools.py
+++ b/metatlas/untargeted/tools.py
@@ -1153,6 +1153,8 @@ def submit_fbmn_jobs(
     overwrite_fbmn: bool,
     output_dir: str,
     skip_fbmn_submit: bool,
+    mirror_raw_data: bool,
+    mirror_mzmine_results: bool,
     direct_input: Optional[str] = None,
     raw_data_dir: Optional[str] = None,
     raw_data_subdir: Optional[str] = None
@@ -1228,8 +1230,10 @@ def submit_fbmn_jobs(
                 
                 # Get mzmine results files and raw data to GNPS2 before starting FBMN job
                 logging.info(tab_print("Ensuring MZmine results are at GNPS2 before submitting FBMN job...", 2))
-                mirror_mzmine_results_to_gnps2(project=project_name,polarity=polarity,output_dir=output_dir,username="bpbowen")
-                mirror_raw_data_to_gnps2(project=project_name,polarity=polarity,username="bpbowen",raw_data_dir=raw_data_dir,raw_data_subdir=raw_data_subdir)
+                if mirror_mzmine_results is True:
+                    mirror_mzmine_results_to_gnps2(project=project_name,polarity=polarity,output_dir=output_dir,username="bpbowen")
+                if mirror_raw_data is True:
+                    mirror_raw_data_to_gnps2(project=project_name,polarity=polarity,username="bpbowen",raw_data_dir=raw_data_dir,raw_data_subdir=raw_data_subdir)
 
                 description = '%s_%s'%(project_name,polarity)
                 spectra_file = f'USERUPLOAD/bpbowen/untargeted_tasks/{project_name}_{polarity}/{project_name}_{polarity}.mgf'
@@ -1874,8 +1878,7 @@ def update_new_untargeted_tasks(
     output_dir: str,
     direct_input: Optional[str] = None,
     raw_data_dir: Optional[str] = None,
-    raw_data_subdir: Optional[str] = None,
-    
+    raw_data_subdir: Optional[str] = None
 ) -> None:
     """
     This script is called by run_mzmine.py before the untargeted pipeline kicks off