Fix module run to allow optional path inputs (#7163)

bentsherman · web-flow · commit 4fd28fd5bfa9 · 2026-05-21T13:03:52.000-05:00
Signed-off-by: Ben Sherman &lt;bentshermann@gmail.com&gt;
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessEntryHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessEntryHandler.groovy
@@ -238,7 +238,7 @@ class ProcessEntryHandler {
     }
 
     /**
-     * Load mapping of input types from the module spec if available. Returns null
+     * Load mapping of input types from the module spec if available. Returns empty map
      * if module spec is absent or unreadable.
      */
     private static Map<String, Class> getModuleSpecInputTypes(Path scriptPath) {
@@ -294,6 +294,10 @@ class ProcessEntryHandler {
         final value = namedArgs.get(name)
 
         if( value == null ) {
+            if( param instanceof FileInParam ) {
+                log.warn "Path input '--${name}' not provided, defaulting to empty list"
+                return []
+            }
             throw new IllegalArgumentException("Missing required parameter: --${name}")
         }
 
@@ -397,6 +401,8 @@ class ProcessEntryHandler {
         final value = namedArgs.get(name)
 
         if( value == null ) {
+            if( param.isOptional() )
+                return null
             throw new IllegalArgumentException("Missing required parameter: --${name}")
         }
 
@@ -433,10 +439,10 @@ class ProcessEntryHandler {
      * Otherwise returns a single file object.
      *
      * @param fileInput String representation of file path(s)
-     * @return Single file object or List of file objects
+     * @return Single file or list of files
      */
     protected Object parseFileInput(String fileInput) {
-        if (fileInput.contains(',')) {
+        if( fileInput.contains(',') ) {
             // Split by comma, trim whitespace, and convert each to a file
             return fileInput.tokenize(',')
                 .collect { it.trim() }
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/ProcessEntryHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/ProcessEntryHandlerTest.groovy
@@ -392,4 +392,75 @@ class ProcessEntryHandlerTest extends Specification {
         '/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 return empty list for missing path input (v1)' () {
+        given:
+        def session = Mock(Session)
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta) {
+            getLocalProcessNames() >> [ 'hello' ]
+        }
+        def handler = new ProcessEntryHandler(script, session, meta)
+        def pathParam = Mock(FileInParam) { getName() >> 'intervals' }
+
+        when: 'the input is not present in params for a path input'
+        def result = handler.getValueForInputV1(pathParam, [:], [:])
+
+        then: 'returns an empty list instead of throwing'
+        result == []
+    }
+
+    def 'should throw error for missing val input (v1)' () {
+        given:
+        def session = Mock(Session)
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta) {
+            getLocalProcessNames() >> [ 'hello' ]
+        }
+        def handler = new ProcessEntryHandler(script, session, meta)
+        def valParam = Mock(ValueInParam) { getName() >> 'id' }
+
+        when: 'a val input is absent'
+        handler.getValueForInputV1(valParam, [:], [:])
+
+        then:
+        def e = thrown(IllegalArgumentException)
+        e.message == 'Missing required parameter: --id'
+    }
+
+    def 'should return null for missing optional input (v2)' () {
+        // Regression test for https://github.com/nextflow-io/nextflow/issues/7161
+        given:
+        def session = Mock(Session)
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta) {
+            getLocalProcessNames() >> [ 'hello' ]
+        }
+        def handler = new ProcessEntryHandler(script, session, meta)
+        def param = new ProcessInput('gzi', Path, true)
+
+        when: 'a v2 optional path input is not provided'
+        def result = handler.getValueForInputV2(param, [:])
+
+        then: 'returns null instead of throwing'
+        result == null
+    }
+
+    def 'should throw error for missing required input (v2)' () {
+        given:
+        def session = Mock(Session)
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta) {
+            getLocalProcessNames() >> [ 'hello' ]
+        }
+        def handler = new ProcessEntryHandler(script, session, meta)
+        def param = new ProcessInput('reads', Path, false)
+
+        when:
+        handler.getValueForInputV2(param, [:])
+
+        then:
+        def e = thrown(IllegalArgumentException)
+        e.message == 'Missing required parameter: --reads'
+    }
 }
