Ignore Azure paths when validating directories

src/main/groovy/nextflow/validation/validators/evaluators/FormatDirectoryPathEvaluator.groovy

@@ -39,7 +39,13 @@ class FormatDirectoryPathEvaluator implements Evaluator {
         if (file instanceof List) {
             return Evaluator.Result.failure("'${value}' is not a directory, but a file path pattern" as String)
         }
-        if (file.exists() && !file.isDirectory()) {
+
+        // Check if this is an Azure storage path
+        def String scheme = file.scheme
+        def boolean isAzurePath = scheme == 'az'
+
+        // For Azure paths, skip the directory check as Azure blob storage doesn't have true directories
+        if (!isAzurePath && file.exists() && !file.isDirectory()) {
             return Evaluator.Result.failure("'${value}' is not a directory, but a file" as String)
         }
         return Evaluator.Result.success()

src/main/groovy/nextflow/validation/validators/evaluators/FormatFilePathEvaluator.groovy

@@ -39,7 +39,13 @@ class FormatFilePathEvaluator implements Evaluator {
         if (file instanceof List) {
             return Evaluator.Result.failure("'${value}' is not a file, but a file path pattern" as String)
         }
-        if (file.exists() && file.isDirectory()) {
+
+        // Check if this is an Azure storage path
+        def String scheme = file.scheme
+        def boolean isAzurePath = scheme == 'az'
+
+        // For Azure paths, skip the directory check as Azure blob storage doesn't have true directories
+        if (!isAzurePath && file.exists() && file.isDirectory()) {
             return Evaluator.Result.failure("'${value}' is not a file, but a directory" as String)
         }
         return Evaluator.Result.success()

src/main/groovy/nextflow/validation/validators/evaluators/FormatFilePathPatternEvaluator.groovy

@@ -41,7 +41,12 @@ class FormatFilePathPatternEvaluator implements Evaluator {
             return Evaluator.Result.failure("No files were found using the glob pattern '${value}'" as String)
         }
         files.each { file ->
-            if (file.isDirectory()) {
+            // Check if this is an Azure storage path
+            def String scheme = file.scheme
+            def boolean isAzurePath = scheme == 'az'
+
+            // For Azure paths, skip the directory check as Azure blob storage doesn't have true directories
+            if (!isAzurePath && file.isDirectory()) {
                 errors.add("'${file.toString()}' is not a file, but a directory" as String)
             }
         }

src/main/groovy/nextflow/validation/validators/evaluators/SchemaEvaluator.groovy

@@ -44,9 +44,14 @@ class SchemaEvaluator implements Evaluator {
 
         // Actual validation logic
         def Path file = Nextflow.file(value)
-        // Don't validate if the file does not exist or is a directory
-        if(!file.exists() || file.isDirectory()) {
-            log.debug("Could not validate the file ${file.toString()}")
+
+        // Check if this is an Azure storage path
+        def String scheme = file.scheme
+        def boolean isAzurePath = scheme == 'az'
+
+        // For non-Azure paths, skip validation if it's a directory
+        if(!isAzurePath && file.exists() && file.isDirectory()) {
+            log.debug("Could not validate the file ${file.toString()} - path is a directory")
             return Evaluator.Result.success()
         }
 

src/test/groovy/nextflow/validation/ValidateParametersTest.groovy

@@ -1397,4 +1397,28 @@ class ValidateParametersTest extends Dsl2Spec{
         noExceptionThrown()
         stdout == ["* --testing: test", "* --genomebutlonger: true"]
     }
+
+    def 'should validate Azure storage file paths' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema_azure_path.json').toAbsolutePath().toString()
+        def SCRIPT = """
+            params.az_file = 'az://mycontainer/myfile.txt'
+            params.az_directory = 'az://mycontainer/mydir/'
+            include { validateParameters } from 'plugin/nf-schema'
+
+            validateParameters(parameters_schema: '$schema')
+        """
+
+        when:
+        def config = [:]
+        def result = new MockScriptRunner(config).setScript(SCRIPT).execute()
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        noExceptionThrown()
+        !stdout
+    }
 }