Add support for comma-separated file paths in ProcessEntryHandler (#6434) [ci fast]

- Add parseFileInput() helper method to handle comma-separated file paths
- Support both String and GString inputs for file parameters
- Return List<Path> for multiple files, single Path for one file
- Handle whitespace trimming and empty string filtering
- Maintain backward compatibility with existing single file behavior
- Add comprehensive unit tests using Spock parameterized testing

Usage:
- Single file: --input file.txt (returns Path object)
- Multiple files: --input "file1.txt,file2.txt,file3.txt" (returns List<Path>)
- With whitespace: --input " file1.txt , file2.txt " (handles gracefully)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-authored-by: Claude <[email protected]>

Author: pditommaso

modules/nextflow/src/main/groovy/nextflow/script/ProcessEntryHandler.groovy

@@ -340,6 +340,27 @@ class ProcessEntryHandler {
         return complexParams
     }
 
+    /**
+     * Parses file input handling comma-separated values.
+     * If the input contains commas, splits and returns a list of files.
+     * Otherwise returns a single file object.
+     * 
+     * @param fileInput String representation of file path(s)
+     * @return Single file object or List of file objects
+     */
+    protected Object parseFileInput(String fileInput) {
+        if (fileInput.contains(',')) {
+            // Split by comma, trim whitespace, and convert each to a file
+            return fileInput.tokenize(',')
+                .collect { it.trim() }
+                .findAll { !it.isEmpty() }
+                .collect { Nextflow.file(it) }
+        } else {
+            // Single file case - existing behavior
+            return Nextflow.file(fileInput)
+        }
+    }
+    
     /**
      * Gets the appropriate value for an input definition, handling type conversion.
      * 
@@ -360,8 +381,8 @@ class ProcessEntryHandler {
         switch( paramType ) {
             case 'path':
             case 'file':
-                if( paramValue instanceof String ) {
-                    return Nextflow.file(paramValue)
+                if( paramValue instanceof String || paramValue instanceof GString ) {
+                    return parseFileInput(paramValue.toString())
                 }
                 return paramValue
 
@@ -376,4 +397,4 @@ class ProcessEntryHandler {
                 return paramValue
         }
     }
-}
+}

modules/nextflow/src/test/groovy/nextflow/script/ProcessEntryHandlerTest.groovy

@@ -16,6 +16,7 @@
 
 package nextflow.script
 
+import java.nio.file.Path
 import nextflow.Session
 import spock.lang.Specification
 
@@ -209,4 +210,43 @@ class ProcessEntryHandlerTest extends Specification {
         // tupleElements[1] should be a Path object (mocked)
         tupleElements[1].toString().contains('file.fa')
     }
-}
+
+    def 'should parse file input correctly' () {
+        given:
+        def session = Mock(Session)
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta)
+        def handler = new ProcessEntryHandler(script, session, meta)
+
+        expect:
+        handler.parseFileInput(INPUT) == EXPECTED_FILES
+
+        where:
+        INPUT                                                             | EXPECTED_FILES
+        '/path/to/file.txt'                                               | Path.of('/path/to/file.txt')
+        and:
+        '/path/to/file1.txt,/path/to/file2.txt,/path/to/file3.txt'        | [Path.of('/path/to/file1.txt'), Path.of('/path/to/file2.txt'), Path.of('/path/to/file3.txt')]
+        ' /path/to/file1.txt , /path/to/file2.txt , /path/to/file3.txt '  | [Path.of('/path/to/file1.txt'), Path.of('/path/to/file2.txt'), Path.of('/path/to/file3.txt')]
+        '/path/to/file1.txt,,/path/to/file2.txt, ,/path/to/file3.txt'     | [Path.of('/path/to/file1.txt'), Path.of('/path/to/file2.txt'), Path.of('/path/to/file3.txt')]
+        'file1.txt,file2.txt'                                             | [Path.of('file1.txt').toAbsolutePath(), Path.of('file2.txt').toAbsolutePath()]
+    }
+
+    def 'should handle file input with GString' () {
+        given:
+        def session = Mock(Session)
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta)
+        def handler = new ProcessEntryHandler(script, session, meta)
+        def inputDef = [name: 'input', type: 'file']
+        def complexParams = [input: "${'/path/to/file1.txt'},${'/path/to/file2.txt'}"]
+
+        when:
+        def result = handler.getValueForInput(inputDef, complexParams)
+
+        then:
+        result instanceof List
+        result.size() == 2
+        result[0].toString().contains('file1.txt')
+        result[1].toString().contains('file2.txt')
+    }
+}