Merge pull request #73 from KarchinLab/dltamayo-dev

Reformat OLGA, make GLIPH2 optional

Author: dltamayo

.cirro/process-form.json

@@ -17,6 +17,12 @@
                 "type": "boolean",
                 "value": true
             },
+            "olga_chunk_length": {
+                "default": 2000000,
+                "description": "Divide total CDR3 list into chunks of n length for processing by OLGA. Larger length = reduced parallelization",
+                "title": "olga_chunk_length",
+                "type": "int"
+            },
             "distance_metric": {
                 "default": "tcrdist",
                 "description": "Use default TCRdist3 or Levenshtein distance metric.",

.cirro/process-input.json

@@ -3,6 +3,7 @@
     "convert_lvl": false,
     "sample_lvl": "$.params.dataset.paramJson.sample_lvl",
     "compare_lvl": "$.params.dataset.paramJson.compare_lvl",
+    "olga_chunk_length": "$.params.dataset.paramJson.olga_chunk_length",
     "matrix_sparsity": "sparse",
     "distance_metric": "$.params.dataset.paramJson.distance_metric",
     "kmer_min_depth": "$.params.dataset.paramJson.kmer_min_depth",

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 
+Copyright (c) 2026 Karchin Lab, Break Through Cancer
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal