Merge pull request #490 from MannLabs/fragment_quant_key_missing

Fix config refactoring bug

alphadia/constants/default.yaml

@@ -307,6 +307,9 @@ search_output:
   # Enable normalization of label-free quantification values
   normalize_lfq: True
 
+  # Save fragment quant matrix for advanced users
+  save_fragment_quant_matrix: False
+
 # Configuration for the optimization of search parameters. These parameters should not normally be adjusted and are for the use of experienced users only.
 optimization:
   # The order in which to perform optimization. Should be a list of lists of parameter names

tests/e2e_tests/e2e_test_cases.yaml

@@ -37,6 +37,9 @@ test_cases:
   - name: multistep
     # see also transfer-dimethyl.md
     config:
+      general:
+        transfer_step_enabled: True
+        mbr_step_enabled: True
       search:
 #        target_num_candidates: # mbr: 3
         target_ms1_tolerance: 4
@@ -53,9 +56,7 @@ test_cases:
         variable_modifications: 'Oxidation@M;Acetyl@Protein_N-term'
         max_var_mod_num: 1 # mbr: 2
         missed_cleavages: 0  # mbr: 1
-      multistep_search:
-        transfer_step_enabled: True
-        mbr_step_enabled: True
+
     # dimethyl data (from tutorial)
     fasta_paths:
       - source_url: https://datashare.biochem.mpg.de/s/1GiKQSwlPf6YlMm/download?path=%2F&files=2024_01_12_human.fasta