Build branch main with version main (c733de2)

Build pipeline: viash-hub.biobox.main-lltcw

Source commit: c733de2e4c

Source message: Bump viash to 0.9.4 (#175)

* Bump viash to 0.9.4

* Add CHANGELOG entry

* Add PR number

target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml

@@ -187,16 +187,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcftools/bcftools_sort"
   executable: "target/nextflow/bcftools/bcftools_sort/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27"
+  viash_version: "0.9.4"
+  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
   git_remote: "https://github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-31-g1efc026"
+  git_tag: "v0.2.0-32-gc733de2"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:

target/nextflow/bcftools/bcftools_sort/main.nf

@@ -1,6 +1,6 @@
 // bcftools_sort main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
       foundClass = "List[${e.foundClass}]"
     }
   } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
     if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
     }
     expectedClass = value instanceof String ? null : "String"
   } else if (par.type == "integer") {
     // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
       try {
-        value = value.toInteger()
+        value = value as Integer
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
       }
     }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
   } else if (par.type == "long") {
     // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
       try {
-        value = value.toLong()
+        value = value as Long
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
       }
     }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
   } else if (par.type == "double") {
     // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
       try {
-        value = value.toDouble()
+        value = value as Double
       } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
       }
     }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
     }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
   } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
     // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
       }
     }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
   } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
     // cast to path if need be
     if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
     expectedClass = value instanceof Path ? null : "Path"
   } else if (par.type == "file" && stage == "input" && par.direction == "output") {
     // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
     }
-    expectedClass = value instanceof String ? null : "String"
   } else {
     // didn't find a match for par.type
     expectedClass = par.type
@@ -3282,16 +3277,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_sort",
-    "viash_version" : "0.9.2",
-    "git_commit" : "1efc0264ca674d8cff7729fcd0ad8f11ea06ee27",
+    "viash_version" : "0.9.4",
+    "git_commit" : "c733de2e4cc21eccb241060f82bce0b332f79d81",
     "git_remote" : "https://github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-31-g1efc026"
+    "git_tag" : "v0.2.0-32-gc733de2"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3696,7 +3691,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   // create process from temp file
   def binding = new nextflow.script.ScriptBinding([:])
   def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
     .setModule(true)
     .setBinding(binding)
   def moduleScript = parser.runScript(tempFile)
@@ -3710,6 +3705,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
   return scriptMeta.getProcess(procKey)
 }
 
+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
   // key to be used to trace the process and determine output names

target/nextflow/bcftools/bcftools_sort/nextflow_schema.json

@@ -37,10 +37,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.output`. Output sorted VCF/BCF file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output sorted VCF/BCF file."
+                "description": "Type: `file`, required, default: `$id.$key.output`. Output sorted VCF/BCF file",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`. Output sorted VCF/BCF file."
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id.$key.output"
             }