feat: Integrate Excel support with SamplesheetConverter

Integrates WorkbookConverter with existing nf-schema pipeline:

Integration Points:
- SamplesheetConverter: Added Excel file detection and processing flow
- Utils.getFileType(): Extended to recognize Excel file extensions
- Seamless fallback to WorkbookConverter for Excel formats

Processing Flow:
1. File type detection identifies Excel formats (xlsx, xlsm, xlsb, xls)
2. WorkbookConverter processes Excel data to List<Map<String,Object>> format  
3. Data flows through existing validation and channel formatting pipeline
4. Full compatibility with JSON schema validation
5. Maintains all existing CSV/TSV/JSON/YAML functionality

Features:
- Transparent Excel processing - users can use Excel files directly
- Sheet selection support via options parameter
- Proper error handling and validation messages
- Zero impact on existing functionality

Addresses GitHub issue #177: Users can now use Excel workbooks directly 
without manual conversion to CSV format.

Author: edmundmiller

plugins/nf-schema/src/main/nextflow/validation/SamplesheetConverter.groovy

@@ -1,6 +1,7 @@
 package nextflow.validation
 
 import groovy.json.JsonSlurper
+import groovy.json.JsonGenerator
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import java.nio.file.Path
@@ -85,19 +86,40 @@ class SamplesheetConverter {
             throw new SchemaValidationException(msg)
         }
 
+        // Handle Excel files first
+        def String fileType = Utils.getFileType(samplesheetFile)
+        def List samplesheetList
+        def JSONArray samplesheet
+
+        if (fileType in ["xlsx", "xlsm", "xlsb", "xls"]) {
+            // Process Excel files: convert to standard format then process like other files
+            def converter = new WorkbookConverter(config)
+            def List<Map<String, Object>> excelData = converter.convertToList(samplesheetFile, options)
+            def castedData = Utils.castToType(excelData) as List
+            samplesheetList = castedData
+
+            // Convert to JSON for validation - same as other formats
+            def jsonGenerator = new JsonGenerator.Options()
+                .excludeNulls()
+                .build()
+            samplesheet = new JSONArray(jsonGenerator.toJson(castedData))
+        } else {
+            // Process other file formats
+            samplesheet = Utils.fileToJsonArray(samplesheetFile, schemaFile, options)
+            samplesheetList = Utils.fileToList(samplesheetFile, schemaFile, options)
+        }
+
         // Validate
         final validator = new JsonSchemaValidator(config)
-        def JSONArray samplesheet = Utils.fileToJsonArray(samplesheetFile, schemaFile, options)
         def List<String> validationErrors = validator.validate(samplesheet, schemaFile.text)
         if (validationErrors) {
             def msg = "${colors.red}The following errors have been detected in ${samplesheetFile.toString()}:\n\n" + validationErrors.join('\n').trim() + "\n${colors.reset}\n"
             log.error("Validation of samplesheet failed!")
             throw new SchemaValidationException(msg, validationErrors)
         }
 
-        // Convert
+        // Convert (already done above for Excel files)
         def LinkedHashMap schemaMap = new JsonSlurper().parseText(schemaFile.text) as LinkedHashMap
-        def List samplesheetList = Utils.fileToList(samplesheetFile, schemaFile, options)
 
         this.rows = []