Update nextflow_schema.json

Adding option to change medaka model.
polio-nanopore · Mar 19, 2024 · 4c63cba · 4c63cba
1 parent ec7545c
commit 4c63cba
Showing 1 changed file with 13 additions and 0 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -93,6 +93,19 @@
         "primer_length": {
           "type": "integer",
           "title": "Length of primer sequences to trim off start and end of reads"
+        },
+        "medaka_model": {
+          "type": "string",
+          "format": "value",
+          "title": "Medaka Model",
+          "description": "Choose the approporiate medaka model for your analysis",
+          "help_text": "The medaka model is chosens depending on whaich flow cell type you have used, what version of Guppy you have used, and what basecalling method you have used",
+          "default": "r941_min_high_g360",
+          "enum": ["r103_fast_g507", "r103_fast_snp_g507", "r103_fast_variant_g507", "r103_hac_g507", "r103_hac_snp_g507", "r103_hac_variant_g507", "r103_min_high_g345", "r103_min_high_g360", "r103_prom_high_g360", "r103_prom_snp_g3210", "r103_prom_variant_g3210", "r103_sup_g507", "r103_sup_snp_g507", "r103_sup_variant_g507", "r1041_e82_260bps_fast_g632", "r1041_e82_260bps_fast_variant_g632", "r1041_e82_260bps_hac_g632", "r1041_e82_260bps_hac_v4.0.0", "r1041_e82_260bps_hac_v4.1.0", "r1041_e82_260bps_hac_variant_g632", "r1041_e82_260bps_hac_variant_v4.1.0", "r1041_e82_260bps_sup_g632", "r1041_e82_260bps_sup_v4.0.0", "r1041_e82_260bps_sup_v4.1.0", "r1041_e82_260bps_sup_variant_g632", "r1041_e82_260bps_sup_variant_v4.1.0", "r1041_e82_400bps_fast_g615", "r1041_e82_400bps_fast_g632", "r1041_e82_400bps_fast_variant_g615", 
+          "r1041_e82_400bps_fast_variant_g632", "r1041_e82_400bps_hac_g615", "r1041_e82_400bps_hac_g632", "r1041_e82_400bps_hac_v4.0.0", "r1041_e82_400bps_hac_v4.1.0", "r1041_e82_400bps_hac_v4.2.0", "r1041_e82_400bps_hac_variant_g615", "r1041_e82_400bps_hac_variant_g632", "r1041_e82_400bps_hac_variant_v4.1.0", "r1041_e82_400bps_hac_variant_v4.2.0", "r1041_e82_400bps_sup_g615", "r1041_e82_400bps_sup_v4.0.0", "r1041_e82_400bps_sup_v4.1.0", "r1041_e82_400bps_sup_v4.2.0", "r1041_e82_400bps_sup_variant_g615", "r1041_e82_400bps_sup_variant_v4.1.0", "r1041_e82_400bps_sup_variant_v4.2.0", "r104_e81_fast_g5015, r104_e81_fast_variant_g5015", "r104_e81_hac_g5015", "r104_e81_hac_variant_g5015", "r104_e81_sup_g5015", "r104_e81_sup_g610", "r104_e81_sup_variant_g610", "r10_min_high_g303", "r10_min_high_g340", "r941_e81_fast_g514",
+          "r941_e81_fast_variant_g514", "r941_e81_hac_g514", "r941_e81_hac_variant_g514", "r941_e81_sup_g514", "r941_e81_sup_variant_g514", "r941_min_fast_g303", "r941_min_fast_g507", "r941_min_fast_snp_g507", "r941_min_fast_variant_g507", "r941_min_hac_g507", "r941_min_hac_snp_g507", "r941_min_hac_variant_g507", "r941_min_high_g303", "r941_min_high_g330", "r941_min_high_g340_rle", "r941_min_high_g344", "r941_min_high_g351", "r941_min_high_g360", "r941_min_sup_g507", "r941_min_sup_snp_g507", "r941_min_sup_variant_g507", "r941_prom_fast_g303", "r941_prom_fast_g507", "r941_prom_fast_snp_g507", "r941_prom_fast_variant_g507", "r941_prom_hac_g507", "r941_prom_hac_snp_g507", "r941_prom_hac_variant_g507", "r941_prom_high_g303", "r941_prom_high_g330", "r941_prom_high_g344", "r941_prom_high_g360", "r941_prom_high_g4011", 
+          "r941_prom_snp_g303", "r941_prom_snp_g322", "r941_prom_snp_g360", "r941_prom_sup_g507", "r941_prom_sup_snp_g507", "r941_prom_sup_variant_g507", "r941_prom_variant_g303", "r941_prom_variant_g322", "r941_prom_variant_g360", "r941_sup_plant_g610", "r941_sup_plant_variant_g610"
+                  ]
         }
       }
     },