update schema

Author: YanyanLiuBio

.gitignore

@@ -16,4 +16,5 @@ temp
 **/old_working
 old_working
 tests/subset.bam
-**/new_not_right
+**/new_not_right
+nextflow_schema.json_old

main.nf

@@ -25,17 +25,14 @@ workflow {
     def pools_ch = Channel.fromList(samplesheetToList(params.pool_sheet, "schemas/input_schema.json"))
 
     def rename_maps = [:]
-    if (params.rename_map) {
-        file(params.rename_map)
-            .readLines()
-            .drop(1)
-            .each { line ->
-                def parts = line.trim().split(",")
-                if (parts.size() == 2) {
-                    rename_maps[parts[0].trim()] = parts[1].trim()
-                }
-            }
+   
+     
+     if (params.rename_map) {
+    def rename_rows = samplesheetToList(params.rename_map, "schemas/rename_map_schema.json")
+        rename_rows.each { row ->
+        rename_maps[row[0]] = row[1]
     }
+     }
     log.info "Rename maps: ${rename_maps}"
 
     LIMA_BOTH_END(pools_ch)

nextflow_schema.json

@@ -27,6 +27,16 @@
                     "fa_icon": "fas fa-folder-open",
                     "format": "directory-path",
                     "type": "string"
+                },
+                "rename_map": {
+                    "description": "Optional CSV file mapping pool_ID.well_ID keys to user-defined sample names.",
+                    "fa_icon": "fas fa-file-csv",
+                    "format": "file-path",
+                    "help_text": "CSV with two columns: 'pool_ID.well_ID' and 'sample_ID'. Each key must follow the format <pool_ID>.<well_ID> where well_ID is [A-H][0-9]{2} (e.g. bc1015.A01). When multiple pools are present, entries for all pools may be included; each pool filters to its own entries by pool_ID prefix. The Barcode column always retains the original pool_ID.well_ID key.",
+                    "mimetype": "text/csv",
+                    "pattern": "^\\S+\\.(csv)$",
+                    "schema": "schemas/rename_map_schema.json",
+                    "type": "string"
                 }
             },
             "required": [
@@ -37,4 +47,4 @@
         }
     },
     "type": "object"
-}
+}

schemas/rename_map_schema.json

@@ -0,0 +1,27 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "title": "rename_map schema",
+    "description": "Schema for the rename_map CSV.",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "pool_ID.well_ID": {
+                "type": "string",
+                "description": "Original barcode key in the format pool_ID.well_ID (e.g. bc1015.A01).",
+                "pattern": "^[A-Za-z0-9]+\\.[A-H][0-9]{2}$",
+                "errorMessage": "pool_ID.well_ID must follow <pool_ID>.<well_ID> where well_ID is a plate coordinate [A-H][0-9]{2}, e.g. bc1015.A01"
+            },
+            "sample_ID": {
+                "type": "string",
+                "description": "User-defined sample name to assign to this well.",
+                "pattern": "^\\S+$",
+                "errorMessage": "sample_ID must be a non-empty string with no whitespace"
+            }
+        },
+        "required": [
+            "pool_ID.well_ID",
+            "sample_ID"
+        ]
+    }
+}