support salvage, drop barcodes.

config/docs/options_README.md

@@ -22,6 +22,7 @@ e.g.*
 `categorize_cell_quality:` *The cell categorization method you would like to use. The methods are described in cell_quality_utils.py in the Pooled Cell Painting Profiling Recipe.  
 e.g.* simple  
 *e.g.* simple_plus  
+*e.g.* salvage  
 `cell_filter:` *Select the categories of cells that you wish to use for analysis.
 Categories are defined in cell_quality_utils.py in the Pooled Cell Painting Profiling Recipe.
 Make sure that the options you set here are available in the categorize_cell_quality method that you set above in core config.  
@@ -121,6 +122,12 @@ e.g.*
 e.g.*  
     - Barcode_BarcodeCalled  
     - Barcode_MatchedTo_ID
+`foci_cols:`*Any barcodes that you want to exclude from any downstream analysis.
+Otherwise, enter false.
+e.g.*  
+    - AAAATTTTCCCCGGGG  
+    - ACTGACTGACTGACTG  
+*e.g.* false
 
 `exact_match_reads_col:`  
 *e.g.* "exact_match_reads_per_cell"

config/options.yaml

@@ -58,6 +58,8 @@ preprocess:
       - Barcode_BarcodeCalled
       - Barcode_MatchedTo_ID
     exact_match_reads_col: "exact_match_reads_per_cell"
+    drop_barcodes:
+      - AAAATTTTCCCCGGGG
   process-cells:
     perform: true
     force_overwrite: true

config/utils/config_utils.py

@@ -88,6 +88,23 @@ def process_additional_options(config=options_config_default):
             "#A157DB",
             "#776244",
         ]
+    elif config["core"]["cell_quality"]["categorize_cell_quality"] == "salvage":
+        config["core"]["cell_quality"]["cell_category_order"] = [
+            "Perfect",
+            "Great",
+            "Salvage-High",
+            "Salvage-Low",
+            "Bad",
+            "Empty",
+        ]
+        config["core"]["cell_quality"]["cell_category_colors"] = [
+            "#DB5F57",
+            "#91DB57",
+            "#57D3DB",
+            "#556FD4",
+            "#A157DB",
+            "#776244",
+        ]
 
     if config["core"]["compression"] == "gzip":
         config["core"]["compression"] = {"method": "gzip", "mtime": 1}