diff --git a/padocc/core/project.py b/padocc/core/project.py
index cccf921..588370a 100644
--- a/padocc/core/project.py
+++ b/padocc/core/project.py
@@ -7,7 +7,7 @@
 import logging
 
 from .errors import error_handler
-from .utils import extract_file, BypassSwitch
+from .utils import extract_file, BypassSwitch, apply_substitutions
 from .logs import reset_file_handler
 
 from .mixins import DirectoryMixin, EvaluationsMixin
@@ -267,7 +267,12 @@ def _configure_filelist(self):
             )
         
         if pattern.endswith('.txt'):
-            self.allfiles.set(extract_file(pattern)) 
+            content = extract_file(pattern)
+            if 'substitutions' in self.base_cfg:
+                content, status = apply_substitutions('datasets', subs=self.base_cfg['substitutions'], content=content)
+                if status:
+                    self.logger.warning(status)
+            self.allfiles.set(content) 
         else:
             # Pattern is a wildcard set of files
             if 'latest' in pattern:
@@ -279,11 +284,13 @@ def _setup_config(
             self, 
             pattern : str = None, 
             update : str = None, 
-            remove : str = None
+            remove : str = None,
+            substitutions: dict = None,
         ) -> None:
         """
         Create base cfg json file with all required parameters.
         """
+
         self.logger.debug('Constructing the config file.')
         if pattern or update or remove:
             config = {
@@ -292,6 +299,8 @@ def _setup_config(
                 'updates':update,
                 'removals':remove,
             }
+            if substitutions:
+                config['substitutions'] = substitutions
             self.base_cfg.set(config)
 
     @property
diff --git a/padocc/core/utils.py b/padocc/core/utils.py
index 6f57df5..65f9992 100644
--- a/padocc/core/utils.py
+++ b/padocc/core/utils.py
@@ -232,4 +232,17 @@ def find_closest(num, closest):
         if abs(d-closest) < min_diff:
             min_diff = abs(d-closest)
             closest_div = d
-    return closest_div
\ No newline at end of file
+    return closest_div
+
+def apply_substitutions(subkey: str, subs: dict = None, content: list = None):
+    if not subs:
+        return content, ""
+
+    if subkey not in subs:
+        return content, f"Subkey {subkey} is not valid for substitutions"
+    
+    content = '\n'.join(content)
+    for f, r in subs[subkey].items():
+        content = content.replace(f,r)
+
+    return content.split('\n') , ""
\ No newline at end of file
diff --git a/padocc/operations/mixins.py b/padocc/operations/mixins.py
index 7612fd6..fd2b6d3 100644
--- a/padocc/operations/mixins.py
+++ b/padocc/operations/mixins.py
@@ -12,9 +12,9 @@
     FalseLogger,
     LoggedOperation
 )
-from padocc.core.utils import extract_file, times
+from padocc.core.utils import extract_file, times, apply_substitutions
 
-from ..core.project import ProjectOperation
+from padocc.core.project import ProjectOperation
 
 config = {
     'proj_code': None,
@@ -117,7 +117,9 @@ def _init_group(self, datasets : list, substitutions: dict = None):
         self.logger.info('Creating project directories')
         # Group config is the contents of datasets.csv
         if substitutions:
-            datasets = _apply_substitutions('init_file',subs=substitutions, content=datasets)
+            datasets, status = apply_substitutions('init_file',subs=substitutions, content=datasets)
+        if status:
+            self.logger.warning(status)
 
         self.datasets.set(datasets)
 
@@ -136,8 +138,14 @@ def _open_json(file):
             proj_code = ds_values[0]
             pattern   = ds_values[1]
 
-            if ds_values[1].endswith('.txt') and substitutions:
-                pattern = _apply_substitutions('dataset_file', subs=substitutions, content=[pattern])[0]
+            if pattern.endswith('.txt') and substitutions:
+                pattern, status = apply_substitutions('dataset_file', subs=substitutions, content=[pattern])
+                pattern = pattern[0]
+                if status:
+                    self.logger.warning(status)
+
+            if substitutions:
+                cfg_values['substitutions'] = substitutions
 
             cfg_values['pattern'] = pattern
             proj_codes.append(proj_code)
@@ -730,16 +738,5 @@ def _get_input(
 
     return config
 
-def _apply_substitutions(subkey: str, subs: dict = None, content: list = None):
-    if not subs:
-        return content, ""
-
-    if subkey not in subs:
-        return content, f"Subkey {subkey} is not valid for substitutions"
-    
-    content = '\n'.join(content)
-    for f, r in subs[subkey].items():
-        content = content.replace(f,r)
-    return content.split('\n')
 
     
\ No newline at end of file