update schema for cutsite

nextflow_schema.json

@@ -714,6 +714,27 @@
                 "save_fragments": {
                     "type": "boolean",
                     "description": "Save fragments files"
+                },
+                "save_digested": {
+                    "type": "boolean",
+                    "description": "Save digested fastq files from cutsite process"
+                },
+                "cutsite": {
+                    "type": "boolean",
+                    "description": "If true, do cutsite process to pre digest reads"
+                },
+                "cutsite_cpu": {
+                    "type": "integer",
+                    "description": "Number of cpu to use for cutsite"
+                },
+                "cutsite_seed": {
+                    "type": "integer",
+                    "description": "Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)"
+                },
+                "cutsite_mode": {
+                    "type": "string",
+                    "description": "Mode to use to make the digestion.",
+                    "enum": ["all", "for_vs_rev", "pile"]
                 }
             }
         }