@nfdi4plants/arctrl 3.1.0 → 3.1.1

package/dist/ts/ts/CWL/Decode.js

@@ -1,24 +1,25 @@
-import { getEnumerator, disposeSafe, Lazy } from '../../node_modules/@fable-org/fable-library-js/Util.js';
-import { length, takeWhile, toArray, delay, collect, append, empty as empty$1, singleton, head as head$1, map as map$2 } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
-import { replace, join, trimEnd, trimStart, toText, interpolate, printf, substring, trim } from '../../node_modules/@fable-org/fable-library-js/String.js';
-import { item } from '../../node_modules/@fable-org/fable-library-js/Array.js';
-import { isMatch } from '../../node_modules/@fable-org/fable-library-js/RegExp.js';
-import { value, map as map$1, unwrap, defaultArg, some, bind } from '../../node_modules/@fable-org/fable-library-js/Option.js';
-import { choose, isEmpty, head, tail, iterate, map, empty, exists, tryPick, cons, singleton as singleton$1, ofArray, tryHead } from '../../node_modules/@fable-org/fable-library-js/List.js';
-import { YAMLElement_Mapping, YAMLElement_Sequence, YAMLElement_Object, YAMLContent_create_Z1C3A29C9, YAMLElement_Value } from '../fable_modules/YAMLicious.1.0.0-alpha.7/YAMLiciousTypes.fs.js';
-import { read, object, string, bool, resizearray, int } from '../fable_modules/YAMLicious.1.0.0-alpha.7/Decode.fs.js';
-import { setProperty, setOptionalProperty } from '../fable_modules/DynamicObj.7.1.0/DynObj.fs.js';
+import { getEnumerator, disposeSafe, defaultOf, comparePrimitives } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { Record, FSharpRef } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { value, map, unwrap, defaultArg, bind, orElseWith } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { record_type, string_type, option_type, array_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { toText, printf, interpolate, substring, replace, trim } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { YAMLElement_Mapping, YAMLElement_Sequence, YAMLElement_Object, YAMLContent_create_Z1C3A29C9, YAMLElement_Value } from '../fable_modules/YAMLicious.1.0.0-alpha.11/YAMLiciousTypes.fs.js';
+import { choose, isEmpty, head, tail, empty, map as map$1, exists, tryPick, mapIndexed, cons, singleton, ofArray, tryHead } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { read, object, string, bool, resizearray, int } from '../fable_modules/YAMLicious.1.0.0-alpha.11/Decode.fs.js';
+import { compare } from '../../node_modules/@fable-org/fable-library-js/BigInt.js';
+import { tryParse } from '../../node_modules/@fable-org/fable-library-js/Boolean.js';
+import { tryParse as tryParse$1 } from '../../node_modules/@fable-org/fable-library-js/Long.js';
+import { tryParse as tryParse$2 } from '../../node_modules/@fable-org/fable-library-js/Double.js';
 import { DynamicObj } from '../fable_modules/DynamicObj.7.1.0/DynamicObj.fs.js';
-import { SchemaSaladString_Literal, SchemaSaladString_Import, SchemaSaladString_Include, SchemaSaladStringModule_toDirectiveString, CWLType_Dirent, DirentInstance, DirectoryInstance_$ctor, FileInstance_$ctor, CWLType_Null, CWLType_Stdout, CWLType_Boolean, CWLType_Double, CWLType_Float, CWLType_Long, CWLType_Int, CWLType_String, CWLType_Directory, CWLType_File, CWLType_Array, InputArraySchema, InputRecordField, InputRecordSchema, InputEnumSchema, CWLType_Union, CWLType_Record, CWLType_Enum, SoftwarePackage, SchemaDefRequirementType } from './CWLTypes.js';
-import { OutputBinding, CWLOutput, OutputSource_Multiple, OutputSource_Single } from './Outputs.js';
-import { InitialWorkDirEntry_StringEntry, InitialWorkDirEntry_DirentEntry, InitialWorkDirEntry_DirectoryEntry, InitialWorkDirEntry_FileEntry, DockerRequirement_create_Z6E6AA686, EnvironmentDef, LoadListingRequirementValue, LoadListingEnum_tryParse_Z721C83C5, ResourceRequirementInstance_$ctor_D76FC00, Requirement_WorkReuseExpressionRequirement, Requirement_WorkReuseRequirement, WorkReuseRequirementValue, Requirement_NetworkAccessExpressionRequirement, Requirement_NetworkAccessRequirement, NetworkAccessRequirementValue, InplaceUpdateRequirementValue, ToolTimeLimitValue_ToolTimeLimitExpression, ToolTimeLimitValue_ToolTimeLimitSeconds, InlineJavascriptRequirementValue, Requirement_StepInputExpressionRequirement, Requirement_MultipleInputFeatureRequirement, Requirement_ScatterFeatureRequirement, Requirement_SubworkflowFeatureRequirement, Requirement_ToolTimeLimitRequirement, Requirement_InplaceUpdateRequirement, Requirement_ResourceRequirement, Requirement_ShellCommandRequirement, Requirement_EnvVarRequirement, Requirement_InitialWorkDirRequirement, Requirement_LoadListingRequirement, Requirement_SoftwareRequirement, Requirement_DockerRequirement, Requirement_SchemaDefRequirement, Requirement_InlineJavascriptRequirement, HintEntry_UnknownHint, HintUnknownValue, HintEntry_KnownHint } from './Requirements.js';
+import { setProperty } from '../fable_modules/DynamicObj.7.1.0/DynObj.fs.js';
+import { LoadListingEnum_tryParse_Z721C83C5, InitialWorkDirEntry_StringEntry, InitialWorkDirEntry_DirentEntry, InitialWorkDirEntry_DirectoryEntry, InitialWorkDirEntry_FileEntry, DockerRequirement, EnvironmentDef, LoadListingRequirementValue, ResourceRequirementInstance, Requirement_WorkReuseExpressionRequirement, Requirement_WorkReuseRequirement, WorkReuseRequirementValue, Requirement_NetworkAccessExpressionRequirement, Requirement_NetworkAccessRequirement, NetworkAccessRequirementValue, InplaceUpdateRequirementValue, ToolTimeLimitValue_ToolTimeLimitExpression, ToolTimeLimitValue_ToolTimeLimitSeconds, InlineJavascriptRequirementValue, Requirement_StepInputExpressionRequirement, Requirement_MultipleInputFeatureRequirement, Requirement_ScatterFeatureRequirement, Requirement_SubworkflowFeatureRequirement, Requirement_ToolTimeLimitRequirement, Requirement_InplaceUpdateRequirement, Requirement_ResourceRequirement, Requirement_ShellCommandRequirement, Requirement_EnvVarRequirement, Requirement_InitialWorkDirRequirement, Requirement_LoadListingRequirement, Requirement_SoftwareRequirement, Requirement_DockerRequirement, Requirement_SchemaDefRequirement, Requirement_InlineJavascriptRequirement, HintEntry_UnknownHint, HintUnknownValue, HintEntry_KnownHint } from './Requirements.js';
+import { FileInstance, DirectoryInstance, SchemaSaladString_Literal, SchemaSaladString_Import, SchemaSaladString_Include, SchemaSaladStringModule_toDirectiveString, DirentInstance, CWLType_Dirent, CWLType_Null, CWLType_Stdout, CWLType_Boolean, CWLType_Double, CWLType_Float, CWLType_Long, CWLType_Int, CWLType_String, CWLType_Directory, CWLType_File, CWLType_Array, InputArraySchema, InputRecordField, InputRecordSchema, InputEnumSchema, CWLType_Union, CWLType_Enum, CWLType_Record, SoftwarePackage, SchemaDefRequirementType, CWLType_file, CWLType_directory } from './CWLTypes.js';
+import { toList, toArray, delay, map as map$2, head as head$1, length } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { OutputBinding, CWLOutput, OutputSource_Single, OutputSource_Multiple } from './Outputs.js';
 import { getItemFromDict } from '../../node_modules/@fable-org/fable-library-js/MapUtil.js';
-import { compare } from '../../node_modules/@fable-org/fable-library-js/BigInt.js';
-import { tryParse } from '../../node_modules/@fable-org/fable-library-js/Long.js';
-import { FSharpRef } from '../../node_modules/@fable-org/fable-library-js/Types.js';
-import { tryParse as tryParse$1 } from '../../node_modules/@fable-org/fable-library-js/Double.js';
+import { unionMany } from '../../node_modules/@fable-org/fable-library-js/Set.js';
 import { InputBinding, CWLInput } from './Inputs.js';
-import { LinkMergeMethod, PickValueMethod, ScatterMethod, StepInput, StepOutput_StepOutputRecord, StepOutputParameter, StepOutput_StepOutputString, WorkflowStepRun_RunString, WorkflowStep } from './WorkflowSteps.js';
+import { LinkMergeMethod, PickValueMethod, ScatterMethod, StepInput, StepOutputParameter, StepOutput_StepOutputRecord, StepOutput_StepOutputString, WorkflowStepRun_RunString, WorkflowStep } from './WorkflowSteps.js';
 import { WorkflowStepRunOps_fromTool, WorkflowStepRunOps_fromOperation, WorkflowStepRunOps_fromExpressionTool, WorkflowStepRunOps_fromWorkflow, CWLProcessingUnit_Operation, CWLProcessingUnit_ExpressionTool, CWLProcessingUnit_Workflow, CWLProcessingUnit_CommandLineTool } from './CWLProcessingUnit.js';
 import { CWLToolDescription } from './ToolDescription.js';
 import { CWLExpressionToolDescription } from './ExpressionToolDescription.js';
@@ -39,79 +40,35 @@ function ResizeArray_map(f, a) {
   }
   return b;
 }
-function Decode_countLeadingSpaces(line) {
-  return length(takeWhile((c) => c === " ", line.split("")));
+class Decode_DecodeWarning extends Record {
+  constructor(Path, Message, Raw) {
+    super();
+    this.Path = Path;
+    this.Message = Message;
+    this.Raw = Raw;
+  }
 }
-function Decode_isBlankLine(line) {
-  return line.trim().length === 0;
+function Decode_DecodeWarning_$reflection() {
+  return record_type("ARCtrl.CWL.Decode.DecodeWarning", [], Decode_DecodeWarning, () => [["Path", string_type], ["Message", string_type], ["Raw", option_type(string_type)]]);
 }
-function Decode_normalizeLineEndings(yaml) {
-  if (yaml == null) {
-    return "";
-  } else {
-    return replace(yaml, "\r\n", "\n");
+class Decode_DecodeResult$1 extends Record {
+  constructor(Value, Warnings) {
+    super();
+    this.Value = Value;
+    this.Warnings = Warnings;
   }
 }
-function Decode_stripLeadingShebang(yaml) {
-  const normalized = Decode_normalizeLineEndings(yaml);
-  const lines = normalized.split("\n");
-  if (lines.length > 0 && item(0, lines).startsWith("#!")) {
-    return join("\n", lines.slice(1, lines.length));
-  } else {
-    return normalized;
-  }
+function Decode_DecodeResult$1_$reflection(gen0) {
+  return record_type("ARCtrl.CWL.Decode.DecodeResult`1", [gen0], Decode_DecodeResult$1, () => [["Value", gen0], ["Warnings", array_type(Decode_DecodeWarning_$reflection())]]);
 }
-function Decode_tryParseBlockScalarHeader(line) {
-  if (Decode_isBlankLine(line)) {
-    return void 0;
-  } else if (isMatch(/^(?:.+:\s*[|>][1-9]?[+-]?\s*(?:#.*)?|-\s*[|>][1-9]?[+-]?\s*(?:#.*)?)$/gu, trimEnd(line))) {
-    return Decode_countLeadingSpaces(line);
+function Decode_addWarning(warnings, path, message, raw) {
+  let clo;
+  if (warnings == null) {
   } else {
-    return void 0;
+    const warningList = value(warnings);
+    void warningList.push(new Decode_DecodeWarning(path, message, map((clo = toText(printf("%A")), clo), raw)));
   }
 }
-function Decode_normalizeYamlInput(yaml) {
-  const normalized = Decode_stripLeadingShebang(yaml);
-  const filtered = [];
-  let blockScalarIndent = void 0;
-  const processLine = (line_mut) => {
-    processLine:
-      while (true) {
-        const line = line_mut;
-        if (blockScalarIndent == null) {
-          const matchValue = Decode_tryParseBlockScalarHeader(line);
-          if (matchValue == null) {
-            if (line === "" ? true : line.trim().length > 0) {
-              void filtered.push(line);
-            }
-          } else {
-            const indent_1 = value(matchValue) | 0;
-            blockScalarIndent = indent_1;
-            void filtered.push(line);
-          }
-        } else {
-          const indent = value(blockScalarIndent) | 0;
-          if (Decode_isBlankLine(line)) {
-            void filtered.push(line);
-          } else if (Decode_countLeadingSpaces(line) > indent) {
-            void filtered.push(line);
-          } else {
-            blockScalarIndent = void 0;
-            line_mut = line;
-            continue processLine;
-          }
-        }
-        break;
-      }
-  };
-  const array = normalized.split("\n");
-  array.forEach(processLine);
-  return trimEnd(join("\n", toArray(filtered)));
-}
-function Decode_removeFullLineComments(yaml) {
-  let array;
-  return join("\n", (array = yaml.split("\n"), array.filter((line) => !trimStart(line).startsWith("#"))));
-}
 function Decode_removeYamlComments(yamlElement) {
   switch (yamlElement.tag) {
     case /* Object */
@@ -193,43 +150,31 @@ function Decode_isRecoverableDecodingError(ex) {
   }
 }
 function Decode_readSanitizedYaml(yaml) {
-  const prepared = Decode_stripLeadingShebang(yaml);
-  const tryRead = (text) => Decode_removeYamlComments(read(text));
-  try {
-    return tryRead(prepared);
-  } catch (matchValue) {
-    if (Decode_isRecoverableDecodingError(matchValue)) {
-      const normalized = Decode_normalizeYamlInput(prepared);
-      try {
-        return tryRead(normalized);
-      } catch (matchValue_1) {
-        if (Decode_isRecoverableDecodingError(matchValue_1)) {
-          return tryRead(Decode_removeFullLineComments(normalized));
-        } else {
-          throw matchValue_1;
-        }
-      }
-    } else {
-      throw matchValue;
-    }
-  }
+  return Decode_removeYamlComments(read(yaml));
+}
+function Decode_boxOverflowInt64(value) {
+  return value;
 }
 function Decode_overflowDecoder(dynObj, dict) {
-  let enumerator = getEnumerator(dict);
-  try {
-    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-      const e = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-      const matchValue = e[1];
-      let matchResult, v, s;
-      if (matchValue.tag === /* Object */
-      3) {
-        if (!isEmpty(matchValue.fields[0])) {
-          switch (head(matchValue.fields[0]).tag) {
+  const decodeOverflowValue = (value_1) => {
+    let collection;
+    let matchResult, v_3, items, other;
+    switch (value_1.tag) {
+      case /* Value */
+      1: {
+        matchResult = 0;
+        v_3 = value_1.fields[0];
+        break;
+      }
+      case /* Object */
+      3: {
+        if (!isEmpty(value_1.fields[0])) {
+          switch (head(value_1.fields[0]).tag) {
             case /* Value */
             1: {
-              if (isEmpty(tail(matchValue.fields[0]))) {
+              if (isEmpty(tail(value_1.fields[0]))) {
                 matchResult = 0;
-                v = head(matchValue.fields[0]).fields[0];
+                v_3 = head(value_1.fields[0]).fields[0];
               } else {
                 matchResult = 2;
               }
@@ -237,9 +182,9 @@ function Decode_overflowDecoder(dynObj, dict) {
             }
             case /* Sequence */
             2: {
-              if (isEmpty(tail(matchValue.fields[0]))) {
+              if (isEmpty(tail(value_1.fields[0]))) {
                 matchResult = 1;
-                s = head(matchValue.fields[0]).fields[0];
+                items = head(value_1.fields[0]).fields[0];
               } else {
                 matchResult = 2;
               }
@@ -251,32 +196,260 @@ function Decode_overflowDecoder(dynObj, dict) {
         } else {
           matchResult = 2;
         }
+        break;
+      }
+      case /* Sequence */
+      2: {
+        matchResult = 1;
+        items = value_1.fields[0];
+        break;
+      }
+      default: {
+        matchResult = 3;
+        other = value_1;
+      }
+    }
+    switch (matchResult) {
+      case 0: {
+        const value$1 = v_3;
+        const matchValue = value$1.Style;
+        let matchResult_1;
+        if (matchValue != null) {
+          switch (value(matchValue).tag) {
+            case /* SingleQuoted */
+            1:
+            case /* DoubleQuoted */
+            2:
+            case /* Block */
+            3: {
+              matchResult_1 = 0;
+              break;
+            }
+            default:
+              matchResult_1 = 1;
+          }
+        } else {
+          matchResult_1 = 1;
+        }
+        switch (matchResult_1) {
+          case 0:
+            return value$1.Value;
+          default: {
+            let matchValue_1;
+            let outArg = false;
+            matchValue_1 = [tryParse(value$1.Value, new FSharpRef(() => outArg, (v) => {
+              outArg = v;
+            })), outArg];
+            if (matchValue_1[0]) {
+              return matchValue_1[1];
+            } else {
+              let matchValue_2;
+              let outArg_1 = 0n;
+              matchValue_2 = [tryParse$1(value$1.Value, 7, false, 64, new FSharpRef(() => outArg_1, (v_1) => {
+                outArg_1 = v_1;
+              })), outArg_1];
+              if (matchValue_2[0]) {
+                return Decode_boxOverflowInt64(matchValue_2[1]);
+              } else {
+                let matchValue_3;
+                let outArg_2 = 0;
+                matchValue_3 = [tryParse$2(value$1.Value, new FSharpRef(() => outArg_2, (v_2) => {
+                  outArg_2 = v_2;
+                })), outArg_2];
+                if (matchValue_3[0]) {
+                  return matchValue_3[1];
+                } else {
+                  return value$1.Value;
+                }
+              }
+            }
+          }
+        }
+      }
+      case 1:
+        return collection = map$1(decodeOverflowValue, items), Array.from(collection);
+      case 2:
+        return Decode_overflowDecoder(new DynamicObj(), object((get$) => get$.Overflow.FieldList(empty()), value_1));
+      default:
+        return other;
+    }
+  };
+  let enumerator = getEnumerator(dict);
+  try {
+    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      const e = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      setProperty(e[0], decodeOverflowValue(e[1]), dynObj);
+    }
+  } finally {
+    disposeSafe(enumerator);
+  }
+  return dynObj;
+}
+function Decode_isIgnorableYamlNoise(value) {
+  let matchResult;
+  switch (value.tag) {
+    case /* Comment */
+    4: {
+      matchResult = 0;
+      break;
+    }
+    case /* Object */
+    3: {
+      if (isEmpty(value.fields[0])) {
+        matchResult = 1;
       } else {
         matchResult = 2;
       }
-      switch (matchResult) {
-        case 0: {
-          setProperty(e[0], v.Value, dynObj);
-          break;
+      break;
+    }
+    default:
+      matchResult = 2;
+  }
+  switch (matchResult) {
+    case 0:
+      return true;
+    case 1:
+      return true;
+    default:
+      return false;
+  }
+}
+function Decode_tryGetPresentField(fieldName, decoder, value) {
+  let matchResult, fields_1;
+  if (value.tag === /* Object */
+  3) {
+    if (exists((_arg) => {
+      let matchResult_1, key_1;
+      if (_arg.tag === /* Mapping */
+      0) {
+        if (_arg.fields[0].Value === fieldName) {
+          matchResult_1 = 0;
+          key_1 = _arg.fields[0];
+        } else {
+          matchResult_1 = 1;
         }
-        case 1: {
-          const newDynObj = new DynamicObj();
-          iterate((x) => {
-            setProperty(e[0], x, dynObj);
-          }, map((arg) => Decode_overflowDecoder(newDynObj, object((get$) => get$.Overflow.FieldList(empty()), arg)), s));
-          break;
+      } else {
+        matchResult_1 = 1;
+      }
+      switch (matchResult_1) {
+        case 0:
+          return true;
+        default:
+          return false;
+      }
+    }, value.fields[0])) {
+      matchResult = 0;
+      fields_1 = value.fields[0];
+    } else {
+      matchResult = 1;
+    }
+  } else {
+    matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0:
+      return object((get$) => {
+        const objectArg = get$.Optional;
+        return objectArg.Field(fieldName, decoder);
+      }, value);
+    default:
+      return void 0;
+  }
+}
+function Decode_tryGetStringField(fieldName, value) {
+  return Decode_tryGetPresentField(fieldName, string, value);
+}
+function Decode_tryGetBoolField(fieldName, value) {
+  return Decode_tryGetPresentField(fieldName, bool, value);
+}
+function Decode_tryGetYamlField(fieldName, value) {
+  return Decode_tryGetPresentField(fieldName, (x) => x, value);
+}
+function Decode_tryGetIntArrayField(fieldName, value) {
+  return Decode_tryGetPresentField(fieldName, (value_1) => resizearray(int, value_1), value);
+}
+function Decode_tryGetInt64Field(fieldName, value) {
+  return Decode_tryGetPresentField(fieldName, (_arg) => {
+    let matchResult, scalar, other;
+    switch (_arg.tag) {
+      case /* Value */
+      1: {
+        matchResult = 0;
+        scalar = _arg.fields[0];
+        break;
+      }
+      case /* Object */
+      3: {
+        if (!isEmpty(_arg.fields[0])) {
+          if (head(_arg.fields[0]).tag === /* Value */
+          1) {
+            if (isEmpty(tail(_arg.fields[0]))) {
+              matchResult = 0;
+              scalar = head(_arg.fields[0]).fields[0];
+            } else {
+              matchResult = 1;
+              other = _arg;
+            }
+          } else {
+            matchResult = 1;
+            other = _arg;
+          }
+        } else {
+          matchResult = 1;
+          other = _arg;
         }
-        case 2: {
-          setProperty(e[0], e[1], dynObj);
-          break;
+        break;
+      }
+      default: {
+        matchResult = 1;
+        other = _arg;
+      }
+    }
+    switch (matchResult) {
+      case 0: {
+        let matchValue;
+        let outArg = 0n;
+        matchValue = [tryParse$1(scalar.Value, 7, false, 64, new FSharpRef(() => outArg, (v) => {
+          outArg = v;
+        })), outArg];
+        if (matchValue[0]) {
+          return matchValue[1];
+        } else {
+          throw new Error(`Invalid int64 value for ${fieldName}: ${scalar.Value}`);
         }
       }
+      default:
+        throw new Error(`Invalid int64 value for ${fieldName}: ${other}`);
     }
-  } finally {
-    disposeSafe(enumerator);
+  }, value);
+}
+function Decode_tryGetLoadListingField(fieldName, value$1) {
+  return map((loadListingValue) => {
+    const matchValue = LoadListingEnum_tryParse_Z721C83C5(loadListingValue);
+    if (matchValue == null) {
+      throw new Error(`Invalid loadListing value '${loadListingValue}'. Expected one of: no_listing, shallow_listing, deep_listing.`);
+    } else {
+      return value(matchValue);
+    }
+  }, Decode_tryGetStringField(fieldName, value$1));
+}
+function Decode_overflowIntoDynamicObj(dynObj, knownFields, value) {
+  if (value.tag === /* Object */
+  3) {
+    object((get$) => Decode_overflowDecoder(dynObj, get$.Overflow.FieldList(knownFields)), value);
   }
   return dynObj;
 }
+function Decode_decodeFileInstanceFields(element) {
+  const file = new FileInstance(unwrap(Decode_tryGetStringField("location", element)), unwrap(Decode_tryGetStringField("path", element)), unwrap(Decode_tryGetStringField("basename", element)), unwrap(Decode_tryGetStringField("dirname", element)), unwrap(Decode_tryGetStringField("nameroot", element)), unwrap(Decode_tryGetStringField("nameext", element)), unwrap(Decode_tryGetStringField("checksum", element)), unwrap(Decode_tryGetInt64Field("size", element)), unwrap(Decode_tryGetYamlField("secondaryFiles", element)), unwrap(Decode_tryGetStringField("format", element)), unwrap(Decode_tryGetStringField("contents", element)));
+  Decode_overflowIntoDynamicObj(file, toList(FileInstance.KnownFieldNames), element);
+  return file;
+}
+function Decode_decodeDirectoryInstanceFields(element) {
+  const directory = new DirectoryInstance(unwrap(Decode_tryGetStringField("location", element)), unwrap(Decode_tryGetStringField("path", element)), unwrap(Decode_tryGetStringField("basename", element)), unwrap(Decode_tryGetYamlField("listing", element)));
+  Decode_overflowIntoDynamicObj(directory, toList(DirectoryInstance.KnownFieldNames), element);
+  return directory;
+}
 function Decode_decodeSchemaSaladString(yEle) {
   let matchResult, v, c, v_1;
   switch (yEle.tag) {
@@ -375,14 +548,18 @@ function Decode_decodeSchemaSaladString(yEle) {
 function Decode_decodeStringOrExpression(yEle) {
   return SchemaSaladStringModule_toDirectiveString(Decode_decodeSchemaSaladString(yEle));
 }
-const Decode_outputBindingGlobDecoder = (value_1) => object((get$) => {
-  let objectArg;
-  return new OutputBinding((objectArg = get$.Optional, objectArg.Field("glob", string)));
-}, value_1);
-const Decode_outputBindingDecoder = (value) => object((get$) => {
+function Decode_outputBindingGlobDecoder(value) {
+  return object((get$) => {
+    let objectArg, objectArg_1, objectArg_2;
+    const binding = new OutputBinding(unwrap((objectArg = get$.Optional, objectArg.Field("glob", string))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("loadContents", bool))), unwrap(Decode_tryGetLoadListingField("loadListing", value)), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("outputEval", string))));
+    Decode_overflowIntoDynamicObj(binding, toList(OutputBinding.KnownFieldNames), value);
+    return binding;
+  }, value);
+}
+const Decode_outputBindingDecoder = (value_1) => object((get$) => {
   const objectArg = get$.Optional;
   return objectArg.Field("outputBinding", Decode_outputBindingGlobDecoder);
-}, value);
+}, value_1);
 function Decode_decodeStringArrayOrScalar(value) {
   let matchResult, items;
   switch (value.tag) {
@@ -416,7 +593,7 @@ function Decode_decodeStringArrayOrScalar(value) {
   }
   switch (matchResult) {
     case 0: {
-      const collection = map(Decode_decodeStringOrExpression, items);
+      const collection = map$1(Decode_decodeStringOrExpression, items);
       return Array.from(collection);
     }
     default:
@@ -427,12 +604,15 @@ const Decode_outputSourceDecoder = (value_1) => object((get$) => {
   const objectArg = get$.Optional;
   return objectArg.Field("outputSource", Decode_decodeStringArrayOrScalar);
 }, value_1);
-const Decode_direntDecoder = (value_1) => object((get$) => {
-  let objectArg, objectArg_1, objectArg_2;
-  return CWLType_Dirent(new DirentInstance((objectArg = get$.Required, objectArg.Field("entry", Decode_decodeSchemaSaladString)), (objectArg_1 = get$.Optional, objectArg_1.Field("entryname", Decode_decodeSchemaSaladString)), (objectArg_2 = get$.Optional, objectArg_2.Field("writable", bool))));
-}, value_1);
+function Decode_direntDecoder(value) {
+  return object((get$) => {
+    let objectArg, objectArg_1, objectArg_2;
+    const dirent = new DirentInstance((objectArg = get$.Required, objectArg.Field("entry", Decode_decodeSchemaSaladString)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("entryname", Decode_decodeSchemaSaladString))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("writable", bool))));
+    Decode_overflowIntoDynamicObj(dirent, toList(DirentInstance.KnownFieldNames), value);
+    return CWLType_Dirent(dirent);
+  }, value);
+}
 function Decode_initialWorkDirEntryDecoder(value$1) {
-  let fileInstance, directoryInstance;
   switch (value$1.tag) {
     case /* Object */
     3: {
@@ -540,9 +720,9 @@ function Decode_initialWorkDirEntryDecoder(value$1) {
         }
         switch (matchResult_2) {
           case 0:
-            return InitialWorkDirEntry_FileEntry((fileInstance = FileInstance_$ctor(), void object((get$) => Decode_overflowDecoder(fileInstance, get$.Overflow.FieldList(empty())), value$1), fileInstance));
+            return InitialWorkDirEntry_FileEntry(Decode_decodeFileInstanceFields(value$1));
           case 1:
-            return InitialWorkDirEntry_DirectoryEntry((directoryInstance = DirectoryInstance_$ctor(), void object((get$_1) => Decode_overflowDecoder(directoryInstance, get$_1.Overflow.FieldList(empty())), value$1), directoryInstance));
+            return InitialWorkDirEntry_DirectoryEntry(Decode_decodeDirectoryInstanceFields(value$1));
           default:
             return InitialWorkDirEntry_StringEntry(Decode_decodeSchemaSaladString(value$1));
         }
@@ -558,9 +738,9 @@ function Decode_initialWorkDirEntryDecoder(value$1) {
 function Decode_cwlSimpleTypeFromString(s) {
   switch (s) {
     case "File":
-      return CWLType_File(FileInstance_$ctor());
+      return CWLType_File(new FileInstance());
     case "Directory":
-      return CWLType_Directory(DirectoryInstance_$ctor());
+      return CWLType_Directory(new DirectoryInstance());
     case "string":
       return CWLType_String();
     case "int":
@@ -587,7 +767,7 @@ function Decode_parseArrayShorthand(typeStr) {
     const matchValue = Decode_parseArrayShorthand(innerType);
     if (matchValue == null) {
       try {
-        return CWLType_Array(new InputArraySchema(Decode_cwlSimpleTypeFromString(innerType), void 0, void 0, void 0));
+        return CWLType_Array(new InputArraySchema(Decode_cwlSimpleTypeFromString(innerType)));
       } catch (matchValue_1) {
         if (Decode_isRecoverableDecodingError(matchValue_1)) {
           return void 0;
@@ -596,46 +776,31 @@ function Decode_parseArrayShorthand(typeStr) {
         }
       }
     } else {
-      return CWLType_Array(new InputArraySchema(value(matchValue), void 0, void 0, void 0));
+      return CWLType_Array(new InputArraySchema(value(matchValue)));
     }
   } else {
     return void 0;
   }
 }
-function inputArraySchemaDecoder$0040324() {
-  return (value_3) => object((get$) => {
+function Decode_inputArraySchemaDecoder(value) {
+  return object((get$) => {
     let objectArg, objectArg_1, objectArg_2, objectArg_3;
-    return new InputArraySchema(Decode_cwlTypeDecoder$0027((objectArg = get$.Required, objectArg.Field("items", (x) => x))), (objectArg_1 = get$.Optional, objectArg_1.Field("label", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", string)));
-  }, value_3);
-}
-const inputArraySchemaDecoder$0040324$002D1 = new Lazy(inputArraySchemaDecoder$0040324);
-function inputRecordFieldDecoder$0040338() {
-  return (value_3) => object((get$) => {
-    let objectArg, objectArg_1, objectArg_2, objectArg_3;
-    return new InputRecordField((objectArg = get$.Required, objectArg.Field("name", string)), Decode_cwlTypeDecoder$0027((objectArg_1 = get$.Required, objectArg_1.Field("type", (x) => x))), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("label", string)));
-  }, value_3);
-}
-const inputRecordFieldDecoder$0040338$002D1 = new Lazy(inputRecordFieldDecoder$0040338);
-function inputRecordSchemaDecoder$0040377() {
-  return (value_3) => object((get$) => {
-    let fieldsElement, objectArg, element, matchValue, objectArg_1, objectArg_2, objectArg_3;
-    return new InputRecordSchema((fieldsElement = (objectArg = get$.Optional, objectArg.Field("fields", (x) => x)), fieldsElement == null ? void 0 : value(fieldsElement).tag === /* Object */
-    3 ? isEmpty(value(fieldsElement).fields[0]) ? [] : (element = value(fieldsElement), matchValue = Decode_tryDecodeFieldsAsArray(element), matchValue == null ? Decode_tryDecodeFieldsAsMap(element) : value(matchValue)) : (element = value(fieldsElement), matchValue = Decode_tryDecodeFieldsAsArray(element), matchValue == null ? Decode_tryDecodeFieldsAsMap(element) : value(matchValue))), (objectArg_1 = get$.Optional, objectArg_1.Field("label", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", string)));
-  }, value_3);
+    const schema = new InputArraySchema(Decode_cwlTypeDecoder$0027((objectArg = get$.Required, objectArg.Field("items", (x) => x))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("label", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("doc", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("name", string))));
+    Decode_overflowIntoDynamicObj(schema, toList(InputArraySchema.KnownFieldNames), value);
+    return schema;
+  }, value);
 }
-const inputRecordSchemaDecoder$0040377$002D1 = new Lazy(inputRecordSchemaDecoder$0040377);
-function inputEnumSchemaDecoder$0040404() {
-  return (value_5) => object((get$) => {
+function Decode_inputRecordFieldDecoder(value) {
+  return object((get$) => {
     let objectArg, objectArg_1, objectArg_2, objectArg_3;
-    return new InputEnumSchema((objectArg = get$.Required, objectArg.Field("symbols", (value) => resizearray(string, value))), (objectArg_1 = get$.Optional, objectArg_1.Field("label", string)), (objectArg_2 = get$.Optional, objectArg_2.Field("doc", string)), (objectArg_3 = get$.Optional, objectArg_3.Field("name", string)));
-  }, value_5);
+    const field = new InputRecordField((objectArg = get$.Required, objectArg.Field("name", string)), Decode_cwlTypeDecoder$0027((objectArg_1 = get$.Required, objectArg_1.Field("type", (x) => x))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("doc", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("label", string))));
+    Decode_overflowIntoDynamicObj(field, toList(InputRecordField.KnownFieldNames), value);
+    return field;
+  }, value);
 }
-const inputEnumSchemaDecoder$0040404$002D1 = new Lazy(inputEnumSchemaDecoder$0040404);
-const Decode_inputArraySchemaDecoder = inputArraySchemaDecoder$0040324$002D1.Value;
-const Decode_inputRecordFieldDecoder = inputRecordFieldDecoder$0040338$002D1.Value;
 function Decode_tryDecodeFieldsAsArray(element) {
   try {
-    return resizearray(inputRecordFieldDecoder$0040338$002D1.Value, element);
+    return resizearray(Decode_inputRecordFieldDecoder, element);
   } catch (matchValue) {
     if (Decode_isRecoverableDecodingError(matchValue)) {
       return void 0;
@@ -651,8 +816,9 @@ function Decode_tryDecodeFieldsAsMap(element) {
     try {
       while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
         const kvp = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-        const fieldType = Decode_cwlTypeDecoder$0027(kvp[1]);
-        void fields.push(new InputRecordField(kvp[0], fieldType, void 0, void 0));
+        const field = new InputRecordField(kvp[0], Decode_cwlTypeDecoder$0027(kvp[1]), unwrap(Decode_tryGetStringField("doc", kvp[1])), unwrap(Decode_tryGetStringField("label", kvp[1])));
+        Decode_overflowIntoDynamicObj(field, toList(InputRecordField.KnownFieldNames), kvp[1]);
+        void fields.push(field);
       }
     } finally {
       disposeSafe(enumerator);
@@ -666,8 +832,29 @@ function Decode_tryDecodeFieldsAsMap(element) {
     }
   }
 }
-const Decode_inputRecordSchemaDecoder = inputRecordSchemaDecoder$0040377$002D1.Value;
-const Decode_inputEnumSchemaDecoder = inputEnumSchemaDecoder$0040404$002D1.Value;
+function Decode_inputRecordSchemaDecoder(value$1) {
+  return object((get$) => {
+    let fieldsElement, objectArg, element, matchValue, objectArg_1, objectArg_2, objectArg_3;
+    const schema = new InputRecordSchema(unwrap((fieldsElement = (objectArg = get$.Optional, objectArg.Field("fields", (x) => x)), fieldsElement == null ? void 0 : value(fieldsElement).tag === /* Object */
+    3 ? isEmpty(value(fieldsElement).fields[0]) ? [] : (element = value(fieldsElement), matchValue = Decode_tryDecodeFieldsAsArray(element), matchValue == null ? Decode_tryDecodeFieldsAsMap(element) : value(matchValue)) : (element = value(fieldsElement), matchValue = Decode_tryDecodeFieldsAsArray(element), matchValue == null ? Decode_tryDecodeFieldsAsMap(element) : value(matchValue)))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("label", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("doc", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("name", string))));
+    Decode_overflowIntoDynamicObj(schema, toList(InputRecordSchema.KnownFieldNames), value$1);
+    return schema;
+  }, value$1);
+}
+function Decode_inputEnumSchemaDecoder(value) {
+  return object((get$) => {
+    let objectArg_1, objectArg_2, objectArg_3;
+    let symbols;
+    const objectArg = get$.Required;
+    symbols = objectArg.Field("symbols", (value_1) => resizearray(string, value_1));
+    if (symbols.length === 0) {
+      throw new Error("CWL enum schema must define at least one symbol.");
+    }
+    const schema = new InputEnumSchema(symbols, unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("label", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("doc", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("name", string))));
+    Decode_overflowIntoDynamicObj(schema, toList(InputEnumSchema.KnownFieldNames), value);
+    return schema;
+  }, value);
+}
 function Decode_cwlTypeDecoder$0027(element) {
   let collection;
   const parseTypeString = (typeStr) => {
@@ -735,7 +922,7 @@ function Decode_cwlTypeDecoder$0027(element) {
     case 0:
       return parseTypeString(v.Value);
     case 1:
-      return CWLType_Union((collection = map(Decode_cwlTypeDecoder$0027, items), Array.from(collection)));
+      return CWLType_Union((collection = map$1(Decode_cwlTypeDecoder$0027, items), Array.from(collection)));
     case 2:
       return object((get$) => {
         let objectArg_1;
@@ -770,7 +957,32 @@ function Decode_cwlTypeDecoder$0027(element) {
         switch (matchResult_1) {
           case 0: {
             const matchValue_1 = v_1.Value;
-            return matchValue_1 === "record" ? CWLType_Record(inputRecordSchemaDecoder$0040377$002D1.Value(element)) : matchValue_1 === "enum" ? CWLType_Enum(inputEnumSchemaDecoder$0040404$002D1.Value(element)) : matchValue_1 === "array" ? CWLType_Array(inputArraySchemaDecoder$0040324$002D1.Value(element)) : parseTypeString(matchValue_1);
+            switch (matchValue_1) {
+              case "record":
+                return CWLType_Record(Decode_inputRecordSchemaDecoder(element));
+              case "enum":
+                return CWLType_Enum(Decode_inputEnumSchemaDecoder(element));
+              case "array":
+                return CWLType_Array(Decode_inputArraySchemaDecoder(element));
+              default: {
+                const typeStr_1 = matchValue_1;
+                const patternInput_1 = typeStr_1.endsWith("?") ? [replace(typeStr_1, "?", ""), true] : [typeStr_1, false];
+                const stripped_1 = patternInput_1[0];
+                const isOptional_1 = patternInput_1[1];
+                switch (stripped_1) {
+                  case "File": {
+                    const baseType_1 = CWLType_File(Decode_decodeFileInstanceFields(element));
+                    return isOptional_1 ? CWLType_Union([CWLType_Null(), baseType_1]) : baseType_1;
+                  }
+                  case "Directory": {
+                    const baseType_2 = CWLType_Directory(Decode_decodeDirectoryInstanceFields(element));
+                    return isOptional_1 ? CWLType_Union([CWLType_Null(), baseType_2]) : baseType_2;
+                  }
+                  default:
+                    return parseTypeString(typeStr_1);
+                }
+              }
+            }
           }
           case 1:
             return Decode_cwlTypeDecoder$0027((objectArg_1 = get$.Required, objectArg_1.Field("type", (x_1) => x_1)));
@@ -791,11 +1003,11 @@ function Decode_cwlTypeStringMatcher(t, get$) {
   if (matchValue == null) {
     switch (newT) {
       case "File": {
-        cwlType = CWLType_File(FileInstance_$ctor());
+        cwlType = CWLType_File(new FileInstance());
         break;
       }
       case "Directory": {
-        cwlType = CWLType_Directory(DirectoryInstance_$ctor());
+        cwlType = CWLType_Directory(new DirectoryInstance());
         break;
       }
       case "Dirent": {
@@ -903,31 +1115,109 @@ const Decode_cwlTypeDecoder = (value_1) => object((get$) => {
     return Decode_cwlTypeStringMatcher(value(cwlType), get$);
   }
 }, value_1);
-const Decode_outputArrayDecoder = (value_1) => object((get$) => {
-  const dict = get$.Overflow.FieldList(empty());
-  const collection = toArray(delay(() => collect((key) => {
-    let v;
-    const value$1 = getItemFromDict(dict, key);
-    const outputBinding = Decode_outputBindingDecoder(value$1);
-    const outputSourceValues = Decode_outputSourceDecoder(value$1);
-    const output = new CWLOutput(key, value$1.tag === /* Object */
-    3 ? !isEmpty(value$1.fields[0]) ? head(value$1.fields[0]).tag === /* Value */
-    1 ? isEmpty(tail(value$1.fields[0])) ? (v = head(value$1.fields[0]).fields[0], Decode_cwlTypeStringMatcher(v.Value, get$)[0]) : Decode_cwlTypeDecoder(value$1)[0] : Decode_cwlTypeDecoder(value$1)[0] : Decode_cwlTypeDecoder(value$1)[0] : Decode_cwlTypeDecoder(value$1)[0]);
-    return append(outputBinding != null ? (setOptionalProperty("outputBinding", outputBinding, output), empty$1()) : empty$1(), delay(() => {
-      let matchValue, values, values_2, values_1, values_3;
-      return append((matchValue = outputSourceValues, matchValue != null ? (values = value(matchValue), values.length > 1) ? (values_2 = value(matchValue), output.OutputSource = OutputSource_Multiple(values_2), empty$1()) : (values_1 = value(matchValue), values_1.length === 1) ? (values_3 = value(matchValue), output.OutputSource = OutputSource_Single(values_3[0]), empty$1()) : empty$1() : empty$1()), delay(() => singleton(output)));
-    }));
-  }, dict.keys())));
-  return Array.from(collection);
-}, value_1);
-const Decode_outputsDecoder = (value) => object((get$) => {
-  const objectArg = get$.Required;
-  return objectArg.Field("outputs", Decode_outputArrayDecoder);
-}, value);
+function Decode_decodeNamedOutput(name, value$1) {
+  let v, values, values_1;
+  const outputBinding = Decode_outputBindingDecoder(value$1);
+  const outputSourceValues = Decode_outputSourceDecoder(value$1);
+  const output = new CWLOutput(name, value$1.tag === /* Object */
+  3 ? !isEmpty(value$1.fields[0]) ? head(value$1.fields[0]).tag === /* Value */
+  1 ? isEmpty(tail(value$1.fields[0])) ? (v = head(value$1.fields[0]).fields[0], Decode_cwlTypeStringMatcher(v.Value, defaultOf())[0]) : Decode_cwlTypeDecoder(value$1)[0] : Decode_cwlTypeDecoder(value$1)[0] : Decode_cwlTypeDecoder(value$1)[0] : Decode_cwlTypeDecoder(value$1)[0], void 0, void 0, unwrap(Decode_tryGetStringField("label", value$1)), unwrap(Decode_tryGetYamlField("secondaryFiles", value$1)), unwrap(Decode_tryGetBoolField("streamable", value$1)), unwrap(Decode_tryGetStringField("doc", value$1)), unwrap(Decode_tryGetStringField("format", value$1)));
+  output.OutputBinding = outputBinding;
+  let matchResult, values_2, values_3;
+  if (outputSourceValues != null) {
+    if (values = value(outputSourceValues), values.length > 1) {
+      matchResult = 0;
+      values_2 = value(outputSourceValues);
+    } else if (values_1 = value(outputSourceValues), values_1.length === 1) {
+      matchResult = 1;
+      values_3 = value(outputSourceValues);
+    } else {
+      matchResult = 2;
+    }
+  } else {
+    matchResult = 2;
+  }
+  switch (matchResult) {
+    case 0: {
+      output.OutputSource = OutputSource_Multiple(values_2);
+      break;
+    }
+    case 1: {
+      output.OutputSource = OutputSource_Single(values_3[0]);
+      break;
+    }
+  }
+  Decode_overflowIntoDynamicObj(output, toList(CWLOutput.KnownFieldNames), value$1);
+  return output;
+}
+function Decode_decodeOutputSequenceItem(warnings, path, index, item) {
+  const matchValue = Decode_tryGetStringField("id", item);
+  if (matchValue == null) {
+    if (Decode_isIgnorableYamlNoise(item)) {
+      return void 0;
+    } else {
+      Decode_addWarning(warnings, `${path}[${index}]`, "Skipped malformed unnamed CWL output entry.", item);
+      return void 0;
+    }
+  } else {
+    return Decode_decodeNamedOutput(value(matchValue), item);
+  }
+}
+function Decode_outputArrayDecoderWithWarnings(warnings, path, value) {
+  let matchResult, items;
+  switch (value.tag) {
+    case /* Object */
+    3: {
+      if (!isEmpty(value.fields[0])) {
+        if (head(value.fields[0]).tag === /* Sequence */
+        2) {
+          if (isEmpty(tail(value.fields[0]))) {
+            matchResult = 0;
+            items = head(value.fields[0]).fields[0];
+          } else {
+            matchResult = 1;
+          }
+        } else {
+          matchResult = 1;
+        }
+      } else {
+        matchResult = 1;
+      }
+      break;
+    }
+    case /* Sequence */
+    2: {
+      matchResult = 0;
+      items = value.fields[0];
+      break;
+    }
+    default:
+      matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0: {
+      const collection = choose((x) => x, mapIndexed((index, item) => Decode_decodeOutputSequenceItem(warnings, path, index, item), items));
+      return Array.from(collection);
+    }
+    default: {
+      const dict = object((get$) => get$.Overflow.FieldList(empty()), value);
+      const collection_1 = toArray(delay(() => map$2((key) => Decode_decodeNamedOutput(key, getItemFromDict(dict, key)), dict.keys())));
+      return Array.from(collection_1);
+    }
+  }
+}
+const Decode_outputArrayDecoder = (value) => Decode_outputArrayDecoderWithWarnings(void 0, "outputs", value);
+function Decode_outputsDecoderWithWarnings(warnings) {
+  return (value_1) => object((get$) => {
+    const objectArg = get$.Required;
+    return objectArg.Field("outputs", (value) => Decode_outputArrayDecoderWithWarnings(warnings, "outputs", value));
+  }, value_1);
+}
+const Decode_outputsDecoder = Decode_outputsDecoderWithWarnings(void 0);
 function Decode_dockerRequirementDecoder(get$) {
   let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6;
-  const dockerFile = map$1(Decode_decodeSchemaSaladString, (objectArg = get$.Optional, objectArg.Field("dockerFile", (x) => x)));
-  return DockerRequirement_create_Z6E6AA686(unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("dockerPull", string))), void 0, unwrap(dockerFile), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("dockerImageId", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("dockerLoad", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("dockerImport", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("dockerOutputDirectory", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("cwltool:dockerRunOptions", Decode_decodeStringArrayOrScalar))));
+  const dockerFile = map(Decode_decodeSchemaSaladString, (objectArg = get$.Optional, objectArg.Field("dockerFile", (x) => x)));
+  return DockerRequirement.create(unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("dockerPull", string))), void 0, unwrap(dockerFile), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("dockerImageId", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("dockerLoad", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("dockerImport", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("dockerOutputDirectory", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("cwltool:dockerRunOptions", Decode_decodeStringArrayOrScalar))));
 }
 function Decode_envVarRequirementDecoder(get$) {
   let envDefElement;
@@ -989,10 +1279,12 @@ function Decode_envVarRequirementDecoder(get$) {
   switch (envDefElement.tag) {
     case /* Sequence */
     2:
-      return resizearray((value_3) => object((get2) => {
+      return resizearray((value_1) => object((get2) => {
         let objectArg_1, objectArg_2;
-        return new EnvironmentDef((objectArg_1 = get2.Required, objectArg_1.Field("envName", string)), (objectArg_2 = get2.Required, objectArg_2.Field("envValue", string)));
-      }, value_3), envDefElement);
+        const env = new EnvironmentDef((objectArg_1 = get2.Required, objectArg_1.Field("envName", string)), (objectArg_2 = get2.Required, objectArg_2.Field("envValue", string)));
+        Decode_overflowIntoDynamicObj(env, toList(EnvironmentDef.KnownFieldNames), value_1);
+        return env;
+      }, value_1), envDefElement);
     case /* Object */
     3: {
       const collection = choose((_arg_2) => {
@@ -1070,18 +1362,20 @@ function Decode_softwareRequirementDecoder(get$) {
   switch (packagesElement.tag) {
     case /* Sequence */
     2:
-      return resizearray((value_5) => object((get2) => {
+      return resizearray((value_1) => object((get2) => {
         let objectArg_1, objectArg_2, objectArg_3;
-        return new SoftwarePackage((objectArg_1 = get2.Required, objectArg_1.Field("package", string)), (objectArg_2 = get2.Optional, objectArg_2.Field("version", (value_1) => resizearray(string, value_1))), (objectArg_3 = get2.Optional, objectArg_3.Field("specs", (value_3) => resizearray(string, value_3))));
-      }, value_5), packagesElement);
+        const package$_1 = new SoftwarePackage((objectArg_1 = get2.Required, objectArg_1.Field("package", string)), unwrap((objectArg_2 = get2.Optional, objectArg_2.Field("version", (value_3) => resizearray(string, value_3)))), unwrap((objectArg_3 = get2.Optional, objectArg_3.Field("specs", (value_5) => resizearray(string, value_5)))));
+        Decode_overflowIntoDynamicObj(package$_1, toList(SoftwarePackage.KnownFieldNames), value_1);
+        return package$_1;
+      }, value_1), packagesElement);
     case /* Object */
     3: {
       const collection = choose((_arg_3) => {
-        let packageName, packageValue, normalizedPackageValue, mappings_1;
+        let packageName, packageValue, normalizedPackageValue, mappings_1, package$;
         if (_arg_3.tag === /* Mapping */
         0) {
           return packageName = _arg_3.fields[0].Value, packageValue = _arg_3.fields[1], normalizedPackageValue = normalizeCollectionElement(packageValue), normalizedPackageValue.tag === /* Object */
-          3 ? isEmpty(normalizedPackageValue.fields[0]) ? new SoftwarePackage(packageName, void 0, void 0) : (mappings_1 = normalizedPackageValue.fields[0], new SoftwarePackage(packageName, tryPick((_arg_1) => {
+          3 ? isEmpty(normalizedPackageValue.fields[0]) ? new SoftwarePackage(packageName) : (mappings_1 = normalizedPackageValue.fields[0], package$ = new SoftwarePackage(packageName, unwrap(tryPick((_arg_1) => {
             let v;
             let matchResult_1, k_1, v_1;
             if (_arg_1.tag === /* Mapping */
@@ -1102,7 +1396,7 @@ function Decode_softwareRequirementDecoder(get$) {
               default:
                 return void 0;
             }
-          }, mappings_1), tryPick((_arg_2) => {
+          }, mappings_1)), unwrap(tryPick((_arg_2) => {
             let v_2;
             let matchResult_2, k_3, v_3;
             if (_arg_2.tag === /* Mapping */
@@ -1123,7 +1417,7 @@ function Decode_softwareRequirementDecoder(get$) {
               default:
                 return void 0;
             }
-          }, mappings_1))) : normalizedPackageValue.tag === /* Sequence */
+          }, mappings_1))), void Decode_overflowIntoDynamicObj(package$, toList(SoftwarePackage.KnownFieldNames), normalizedPackageValue), package$) : normalizedPackageValue.tag === /* Sequence */
           2 ? new SoftwarePackage(packageName, void 0, decodeSpecsArray(normalizedPackageValue)) : new SoftwarePackage(packageName, void 0, [Decode_decodeStringOrExpression(packageValue)]);
         } else {
           return void 0;
@@ -1228,7 +1522,7 @@ function Decode_decodeResourceScalar(element) {
     const scalarValue = value(matchValue);
     let matchValue_1;
     let outArg = 0n;
-    matchValue_1 = [tryParse(scalarValue, 7, false, 64, new FSharpRef(() => outArg, (v) => {
+    matchValue_1 = [tryParse$1(scalarValue, 7, false, 64, new FSharpRef(() => outArg, (v) => {
       outArg = v;
     })), outArg];
     if (matchValue_1[0]) {
@@ -1236,7 +1530,7 @@ function Decode_decodeResourceScalar(element) {
     } else {
       let matchValue_2;
       let outArg_1 = 0;
-      matchValue_2 = [tryParse$1(scalarValue, new FSharpRef(() => outArg_1, (v_1) => {
+      matchValue_2 = [tryParse$2(scalarValue, new FSharpRef(() => outArg_1, (v_1) => {
         outArg_1 = v_1;
       })), outArg_1];
       if (matchValue_2[0]) {
@@ -1249,21 +1543,28 @@ function Decode_decodeResourceScalar(element) {
 }
 function Decode_optionalResourceField(get$, fieldName) {
   let objectArg;
-  return map$1(Decode_decodeResourceScalar, (objectArg = get$.Optional, objectArg.Field(fieldName, (x) => x)));
+  return map(Decode_decodeResourceScalar, (objectArg = get$.Optional, objectArg.Field(fieldName, (x) => x)));
 }
 function Decode_resourceRequirementDecoder(get$) {
-  return ResourceRequirementInstance_$ctor_D76FC00(some(Decode_optionalResourceField(get$, "coresMin")), some(Decode_optionalResourceField(get$, "coresMax")), some(Decode_optionalResourceField(get$, "ramMin")), some(Decode_optionalResourceField(get$, "ramMax")), some(Decode_optionalResourceField(get$, "tmpdirMin")), some(Decode_optionalResourceField(get$, "tmpdirMax")), some(Decode_optionalResourceField(get$, "outdirMin")), some(Decode_optionalResourceField(get$, "outdirMax")));
+  return new ResourceRequirementInstance(Decode_optionalResourceField(get$, "coresMin"), Decode_optionalResourceField(get$, "coresMax"), Decode_optionalResourceField(get$, "ramMin"), Decode_optionalResourceField(get$, "ramMax"), Decode_optionalResourceField(get$, "tmpdirMin"), Decode_optionalResourceField(get$, "tmpdirMax"), Decode_optionalResourceField(get$, "outdirMin"), Decode_optionalResourceField(get$, "outdirMax"));
 }
 function Decode_schemaDefRequirementTypeDecoder(value) {
   const dict = object((get$) => get$.Overflow.FieldList(empty()), value);
+  const schemaDefKnownFields = toList(unionMany([SchemaDefRequirementType.KnownFieldNames, InputRecordSchema.KnownFieldNames, InputArraySchema.KnownFieldNames, InputEnumSchema.KnownFieldNames], {
+    Compare: comparePrimitives
+  }));
   if (dict.has("name")) {
-    return new SchemaDefRequirementType(Decode_decodeStringOrExpression(getItemFromDict(dict, "name")), Decode_cwlTypeDecoder$0027(value));
+    const schema = new SchemaDefRequirementType(Decode_decodeStringOrExpression(getItemFromDict(dict, "name")), Decode_cwlTypeDecoder$0027(value));
+    Decode_overflowIntoDynamicObj(schema, schemaDefKnownFields, value);
+    return schema;
   } else {
     if (dict.size === 0) {
       throw new Error("SchemaDefRequirement entry cannot be empty.");
     }
     const kv = head$1(dict);
-    return new SchemaDefRequirementType(kv[0], Decode_cwlTypeDecoder$0027(kv[1]));
+    const schema_1 = new SchemaDefRequirementType(kv[0], Decode_cwlTypeDecoder$0027(kv[1]));
+    Decode_overflowIntoDynamicObj(schema_1, cons(kv[0], schemaDefKnownFields), value);
+    return schema_1;
   }
 }
 function Decode_schemaDefRequirementDecoder(get$) {
@@ -1367,7 +1668,7 @@ function Decode_toolTimeLimitRequirementDecoder(get$) {
   } else {
     let matchValue;
     let outArg = 0n;
-    matchValue = [tryParse(value(tryGetScalarString), 7, false, 64, new FSharpRef(() => outArg, (v) => {
+    matchValue = [tryParse$1(value(tryGetScalarString), 7, false, 64, new FSharpRef(() => outArg, (v) => {
       outArg = v;
     })), outArg];
     if (matchValue[0]) {
@@ -1383,7 +1684,7 @@ function Decode_toolTimeLimitRequirementDecoder(get$) {
 }
 function Decode_inlineJavascriptRequirementDecoder(get$) {
   let objectArg;
-  return new InlineJavascriptRequirementValue((objectArg = get$.Optional, objectArg.Field("expressionLib", Decode_decodeStringArrayOrScalar)));
+  return new InlineJavascriptRequirementValue(unwrap((objectArg = get$.Optional, objectArg.Field("expressionLib", Decode_decodeStringArrayOrScalar))));
 }
 function Decode_requirementFromTypeName(cls, get$) {
   switch (cls) {
@@ -1429,6 +1730,56 @@ function Decode_requirementFromTypeName(cls, get$) {
       throw new Error(`Invalid or unsupported requirement class: ${cls}`);
   }
 }
+function Decode_addRequirementPayloadOverflow(element, requirement) {
+  const knownWithClass = (knownFields) => cons("class", toList(knownFields));
+  switch (requirement.tag) {
+    case /* InlineJavascriptRequirement */
+    0: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(InlineJavascriptRequirementValue.KnownFieldNames), element);
+      break;
+    }
+    case /* DockerRequirement */
+    2: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(DockerRequirement.KnownFieldNames), element);
+      break;
+    }
+    case /* LoadListingRequirement */
+    4: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(LoadListingRequirementValue.KnownFieldNames), element);
+      break;
+    }
+    case /* EnvVarRequirement */
+    6: {
+      break;
+    }
+    case /* SoftwareRequirement */
+    3: {
+      break;
+    }
+    case /* ResourceRequirement */
+    8: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(ResourceRequirementInstance.KnownFieldNames), element);
+      break;
+    }
+    case /* WorkReuseRequirement */
+    9: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(WorkReuseRequirementValue.KnownFieldNames), element);
+      break;
+    }
+    case /* NetworkAccessRequirement */
+    11: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(NetworkAccessRequirementValue.KnownFieldNames), element);
+      break;
+    }
+    case /* InplaceUpdateRequirement */
+    13: {
+      Decode_overflowIntoDynamicObj(requirement.fields[0], knownWithClass(InplaceUpdateRequirementValue.KnownFieldNames), element);
+      break;
+    }
+    default:
+  }
+  return requirement;
+}
 function Decode_requirementArrayDecoder(yEle) {
   let matchResult, items, other;
   if (yEle.tag === /* Object */
@@ -1454,15 +1805,15 @@ function Decode_requirementArrayDecoder(yEle) {
   }
   switch (matchResult) {
     case 0: {
-      const collection = map((ele) => object((get$) => {
+      const collection = map$1((ele) => object((get$) => {
         let objectArg;
-        return Decode_requirementFromTypeName((objectArg = get$.Required, objectArg.Field("class", string)), get$);
+        return Decode_addRequirementPayloadOverflow(ele, Decode_requirementFromTypeName((objectArg = get$.Required, objectArg.Field("class", string)), get$));
       }, ele), items);
       return Array.from(collection);
     }
     case 1:
       return object((get$_1) => {
-        const collection_1 = map$2((kv) => object((get$_2) => Decode_requirementFromTypeName(kv[0], get$_2), kv[1]), get$_1.Overflow.FieldList(empty()));
+        const collection_1 = map$2((kv) => Decode_addRequirementPayloadOverflow(kv[1], object((get$_2) => Decode_requirementFromTypeName(kv[0], get$_2), kv[1])), get$_1.Overflow.FieldList(empty()));
         return Array.from(collection_1);
       }, yEle);
     default:
@@ -1473,7 +1824,7 @@ function Decode_tryDecodeKnownRequirementFromElement(element) {
   try {
     return object((get$) => {
       let objectArg;
-      return Decode_requirementFromTypeName((objectArg = get$.Required, objectArg.Field("class", string)), get$);
+      return Decode_addRequirementPayloadOverflow(element, Decode_requirementFromTypeName((objectArg = get$.Required, objectArg.Field("class", string)), get$));
     }, element);
   } catch (ex) {
     let hintClass;
@@ -1544,7 +1895,7 @@ function Decode_hintArrayDecoder(yEle) {
   }
   switch (matchResult) {
     case 0: {
-      const collection = map(Decode_decodeHintElement, items);
+      const collection = map$1(Decode_decodeHintElement, items);
       return Array.from(collection);
     }
     case 1:
@@ -1571,7 +1922,7 @@ function Decode_hintArrayDecoder(yEle) {
               default:
                 return false;
             }
-          }, mappings) ? kv[1] : YAMLElement_Object(cons(YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("class"), YAMLElement_Object(singleton$1(YAMLElement_Value(YAMLContent_create_Z1C3A29C9(kv[0]))))), mappings))) : YAMLElement_Object(ofArray([YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("class"), YAMLElement_Object(singleton$1(YAMLElement_Value(YAMLContent_create_Z1C3A29C9(kv[0]))))), YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("value"), matchValue)]))));
+          }, mappings) ? kv[1] : YAMLElement_Object(cons(YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("class"), YAMLElement_Object(singleton(YAMLElement_Value(YAMLContent_create_Z1C3A29C9(kv[0]))))), mappings))) : YAMLElement_Object(ofArray([YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("class"), YAMLElement_Object(singleton(YAMLElement_Value(YAMLContent_create_Z1C3A29C9(kv[0]))))), YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("value"), matchValue)]))));
         }, get$.Overflow.FieldList(empty()));
         return Array.from(collection_1);
       }, yEle);
@@ -1587,115 +1938,93 @@ const Decode_hintsDecoder = (value) => object((get$) => {
   const objectArg = get$.Optional;
   return objectArg.Field("hints", Decode_hintArrayDecoder);
 }, value);
-const Decode_inputBindingDecoder = (value_5) => object((get$) => {
+const Decode_inputBindingDecoder = (value_9) => object((get$) => {
   const objectArg = get$.Optional;
-  return objectArg.Field("inputBinding", (value_4) => object((get$0027) => {
-    let objectArg_1, objectArg_2, objectArg_3, objectArg_4;
-    return new InputBinding((objectArg_1 = get$0027.Optional, objectArg_1.Field("prefix", string)), (objectArg_2 = get$0027.Optional, objectArg_2.Field("position", int)), (objectArg_3 = get$0027.Optional, objectArg_3.Field("itemSeparator", string)), (objectArg_4 = get$0027.Optional, objectArg_4.Field("separate", bool)));
-  }, value_4));
-}, value_5);
-const Decode_inputArrayDecoder = (value_1) => object((get$) => {
-  const dict = get$.Overflow.FieldList(empty());
-  const collection = toArray(delay(() => collect((key) => {
-    const value = getItemFromDict(dict, key);
-    const inputBinding = Decode_inputBindingDecoder(value);
-    let patternInput;
-    let matchResult, v, mappings;
-    if (value.tag === /* Object */
-    3) {
+  return objectArg.Field("inputBinding", (value) => object((get$0027) => {
+    let objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, objectArg_7;
+    const binding = new InputBinding(unwrap((objectArg_1 = get$0027.Optional, objectArg_1.Field("prefix", string))), unwrap((objectArg_2 = get$0027.Optional, objectArg_2.Field("position", int))), unwrap((objectArg_3 = get$0027.Optional, objectArg_3.Field("itemSeparator", string))), unwrap((objectArg_4 = get$0027.Optional, objectArg_4.Field("separate", bool))), unwrap((objectArg_5 = get$0027.Optional, objectArg_5.Field("loadContents", bool))), unwrap((objectArg_6 = get$0027.Optional, objectArg_6.Field("valueFrom", string))), unwrap((objectArg_7 = get$0027.Optional, objectArg_7.Field("shellQuote", bool))));
+    Decode_overflowIntoDynamicObj(binding, toList(InputBinding.KnownFieldNames), value);
+    return binding;
+  }, value));
+}, value_9);
+function Decode_decodeNamedInput(name, value) {
+  let v;
+  const inputBinding = Decode_inputBindingDecoder(value);
+  const patternInput = value.tag === /* Object */
+  3 ? !isEmpty(value.fields[0]) ? head(value.fields[0]).tag === /* Value */
+  1 ? isEmpty(tail(value.fields[0])) ? (v = head(value.fields[0]).fields[0], Decode_cwlTypeStringMatcher(v.Value, defaultOf())) : Decode_cwlTypeDecoder(value) : Decode_cwlTypeDecoder(value) : Decode_cwlTypeDecoder(value) : Decode_cwlTypeDecoder(value);
+  const input = new CWLInput(name, patternInput[0], void 0, void 0, unwrap(Decode_tryGetStringField("label", value)), unwrap(Decode_tryGetYamlField("secondaryFiles", value)), unwrap(Decode_tryGetBoolField("streamable", value)), unwrap(Decode_tryGetStringField("doc", value)), unwrap(Decode_tryGetStringField("format", value)), unwrap(Decode_tryGetBoolField("loadContents", value)), unwrap(Decode_tryGetLoadListingField("loadListing", value)), unwrap(Decode_tryGetYamlField("default", value)));
+  if (patternInput[1]) {
+    input.Optional = true;
+  }
+  input.InputBinding = inputBinding;
+  Decode_overflowIntoDynamicObj(input, toList(CWLInput.KnownFieldNames), value);
+  return input;
+}
+function Decode_decodeInputSequenceItem(warnings, path, index, item) {
+  const matchValue = Decode_tryGetStringField("id", item);
+  if (matchValue == null) {
+    if (Decode_isIgnorableYamlNoise(item)) {
+      return void 0;
+    } else {
+      Decode_addWarning(warnings, `${path}[${index}]`, "Skipped malformed unnamed CWL input entry.", item);
+      return void 0;
+    }
+  } else {
+    return Decode_decodeNamedInput(value(matchValue), item);
+  }
+}
+function Decode_inputArrayDecoderWithWarnings(warnings, path, value) {
+  let matchResult, items;
+  switch (value.tag) {
+    case /* Object */
+    3: {
       if (!isEmpty(value.fields[0])) {
-        if (head(value.fields[0]).tag === /* Value */
-        1) {
+        if (head(value.fields[0]).tag === /* Sequence */
+        2) {
           if (isEmpty(tail(value.fields[0]))) {
             matchResult = 0;
-            v = head(value.fields[0]).fields[0];
+            items = head(value.fields[0]).fields[0];
           } else {
             matchResult = 1;
-            mappings = value.fields[0];
           }
         } else {
           matchResult = 1;
-          mappings = value.fields[0];
         }
       } else {
         matchResult = 1;
-        mappings = value.fields[0];
       }
-    } else {
-      matchResult = 2;
+      break;
     }
-    switch (matchResult) {
-      case 0: {
-        patternInput = Decode_cwlTypeStringMatcher(v.Value, get$);
-        break;
-      }
-      case 1: {
-        if (exists((m) => {
-          let matchResult_1, k_1;
-          if (m.tag === /* Mapping */
-          0) {
-            if (m.fields[0].Value === "type") {
-              matchResult_1 = 0;
-              k_1 = m.fields[0];
-            } else {
-              matchResult_1 = 1;
-            }
-          } else {
-            matchResult_1 = 1;
-          }
-          switch (matchResult_1) {
-            case 0:
-              return true;
-            default:
-              return false;
-          }
-        }, mappings)) {
-          patternInput = Decode_cwlTypeDecoder(value);
-        } else {
-          let matchResult_2, v_1;
-          if (value.tag === /* Object */
-          3) {
-            if (!isEmpty(value.fields[0])) {
-              if (head(value.fields[0]).tag === /* Value */
-              1) {
-                if (isEmpty(tail(value.fields[0]))) {
-                  matchResult_2 = 0;
-                  v_1 = head(value.fields[0]).fields[0];
-                } else {
-                  matchResult_2 = 1;
-                }
-              } else {
-                matchResult_2 = 1;
-              }
-            } else {
-              matchResult_2 = 1;
-            }
-          } else {
-            matchResult_2 = 1;
-          }
-          switch (matchResult_2) {
-            case 0: {
-              patternInput = Decode_cwlTypeStringMatcher(v_1.Value, get$);
-              break;
-            }
-            default:
-              throw new Error("Unexpected input format without type field");
-          }
-        }
-        break;
-      }
-      default:
-        throw new Error("Unexpected input format in inputArrayDecoder");
+    case /* Sequence */
+    2: {
+      matchResult = 0;
+      items = value.fields[0];
+      break;
     }
-    const input = new CWLInput(key, patternInput[0]);
-    return append(patternInput[1] ? (setOptionalProperty("optional", true, input), empty$1()) : empty$1(), delay(() => append(inputBinding != null ? (setOptionalProperty("inputBinding", inputBinding, input), empty$1()) : empty$1(), delay(() => singleton(input)))));
-  }, dict.keys())));
-  return Array.from(collection);
-}, value_1);
-const Decode_inputsDecoder = (value) => object((get$) => {
-  const objectArg = get$.Optional;
-  return objectArg.Field("inputs", Decode_inputArrayDecoder);
-}, value);
+    default:
+      matchResult = 1;
+  }
+  switch (matchResult) {
+    case 0: {
+      const collection = choose((x) => x, mapIndexed((index, item) => Decode_decodeInputSequenceItem(warnings, path, index, item), items));
+      return Array.from(collection);
+    }
+    default: {
+      const dict = object((get$) => get$.Overflow.FieldList(empty()), value);
+      const collection_1 = toArray(delay(() => map$2((key) => Decode_decodeNamedInput(key, getItemFromDict(dict, key)), dict.keys())));
+      return Array.from(collection_1);
+    }
+  }
+}
+const Decode_inputArrayDecoder = (value) => Decode_inputArrayDecoderWithWarnings(void 0, "inputs", value);
+function Decode_inputsDecoderWithWarnings(warnings) {
+  return (value_1) => object((get$) => {
+    const objectArg = get$.Optional;
+    return objectArg.Field("inputs", (value) => Decode_inputArrayDecoderWithWarnings(warnings, "inputs", value));
+  }, value_1);
+}
+const Decode_inputsDecoder = Decode_inputsDecoderWithWarnings(void 0);
 const Decode_baseCommandDecoder = (value_2) => object((get$) => {
   let baseCommandField;
   const objectArg = get$.Optional;
@@ -1928,13 +2257,16 @@ function Decode_scatterMethodFieldDecoder(field) {
 function Decode_expressionStringOptionFieldDecoder(field) {
   return (value) => object((get$) => {
     let objectArg;
-    return map$1(Decode_decodeStringOrExpression, (objectArg = get$.Optional, objectArg.Field(field, (x) => x)));
+    return map(Decode_decodeStringOrExpression, (objectArg = get$.Optional, objectArg.Field(field, (x) => x)));
   }, value);
 }
 function Decode_decodeStepInputFromValue(id, value$1, allowScalarSource) {
   const scalarSource = allowScalarSource ? Decode_stringOrStringArrayDecoder(value$1) : void 0;
   const fieldSource = Decode_sourceArrayFieldDecoder("source")(value$1);
-  return new StepInput(id, scalarSource != null ? value(scalarSource) : fieldSource != null ? value(fieldSource) : void 0, Decode_yamlElementOptionFieldDecoder("default")(value$1), Decode_stringOptionFieldDecoder("valueFrom")(value$1), Decode_linkMergeFieldDecoder("linkMerge")(value$1), Decode_pickValueFieldDecoder("pickValue")(value$1), Decode_stringOptionFieldDecoder("doc")(value$1), Decode_boolOptionFieldDecoder("loadContents")(value$1), Decode_stringOptionFieldDecoder("loadListing")(value$1), Decode_stringOptionFieldDecoder("label")(value$1));
+  const source = scalarSource != null ? value(scalarSource) : fieldSource != null ? value(fieldSource) : void 0;
+  const stepInput = StepInput.create(id, unwrap(source), unwrap(Decode_yamlElementOptionFieldDecoder("default")(value$1)), unwrap(Decode_stringOptionFieldDecoder("valueFrom")(value$1)), unwrap(Decode_linkMergeFieldDecoder("linkMerge")(value$1)), unwrap(Decode_pickValueFieldDecoder("pickValue")(value$1)), unwrap(Decode_stringOptionFieldDecoder("doc")(value$1)), unwrap(Decode_boolOptionFieldDecoder("loadContents")(value$1)), unwrap(Decode_stringOptionFieldDecoder("loadListing")(value$1)), unwrap(Decode_stringOptionFieldDecoder("label")(value$1)));
+  Decode_overflowIntoDynamicObj(stepInput, toList(StepInput.KnownFieldNames), value$1);
+  return stepInput;
 }
 function Decode_decodeStepInputsFromMap(value) {
   const dict = object((get$) => get$.Overflow.FieldList(empty()), value);
@@ -1944,11 +2276,26 @@ function Decode_decodeStepInputsFromMap(value) {
 function Decode_decodeStepInputFromArrayItem(item) {
   return Decode_decodeStepInputFromValue(Decode_stringFieldDecoder("id")(item), item, false);
 }
-function Decode_decodeStepInputsFromArray(items) {
-  const collection = map(Decode_decodeStepInputFromArrayItem, items);
+function Decode_decodeStepInputsFromArrayWithWarnings(warnings, path, items) {
+  const collection = choose((x) => x, mapIndexed((index, item) => {
+    const matchValue = Decode_tryGetStringField("id", item);
+    if (matchValue == null) {
+      if (Decode_isIgnorableYamlNoise(item)) {
+        return void 0;
+      } else {
+        Decode_addWarning(warnings, `${path}[${index}]`, "Skipped malformed unnamed CWL step input entry.", item);
+        return void 0;
+      }
+    } else {
+      return Decode_decodeStepInputFromArrayItem(item);
+    }
+  }, items));
   return Array.from(collection);
 }
-function Decode_inputStepDecoder(value) {
+function Decode_decodeStepInputsFromArray(items) {
+  return Decode_decodeStepInputsFromArrayWithWarnings(void 0, "in", items);
+}
+function Decode_inputStepDecoderWithWarnings(warnings, path, value) {
   let matchResult, items;
   switch (value.tag) {
     case /* Object */
@@ -1981,11 +2328,12 @@ function Decode_inputStepDecoder(value) {
   }
   switch (matchResult) {
     case 0:
-      return Decode_decodeStepInputsFromArray(items);
+      return Decode_decodeStepInputsFromArrayWithWarnings(warnings, path, items);
     default:
       return Decode_decodeStepInputsFromMap(value);
   }
 }
+const Decode_inputStepDecoder = (value) => Decode_inputStepDecoderWithWarnings(void 0, "in", value);
 function Decode_decodeStepOutputItem(value) {
   let matchResult, v;
   switch (value.tag) {
@@ -2020,8 +2368,12 @@ function Decode_decodeStepOutputItem(value) {
   switch (matchResult) {
     case 0:
       return StepOutput_StepOutputString(v.Value);
-    default:
-      return StepOutput_StepOutputRecord(new StepOutputParameter(Decode_stringFieldDecoder("id")(value)));
+    default: {
+      const id = Decode_stringFieldDecoder("id")(value);
+      const output = StepOutputParameter.create(id);
+      Decode_overflowIntoDynamicObj(output, toList(StepOutputParameter.KnownFieldNames), value);
+      return StepOutput_StepOutputRecord(output);
+    }
   }
 }
 const Decode_outputStepsDecoder = (value_2) => object((get$) => {
@@ -2101,7 +2453,7 @@ const Decode_outputStepsDecoder = (value_2) => object((get$) => {
     case 2:
       return [];
     case 3: {
-      const collection = map(Decode_decodeStepOutputItem, outputs);
+      const collection = map$1(Decode_decodeStepOutputItem, outputs);
       return Array.from(collection);
     }
     default:
@@ -2160,13 +2512,13 @@ function Decode_withDefaultCwlVersion(defaultCwlVersion, yamlElement) {
       return yamlElement;
     } else {
       const fields_2 = yamlElement.fields[0];
-      return YAMLElement_Object(cons(YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("cwlVersion"), YAMLElement_Object(singleton$1(YAMLElement_Value(YAMLContent_create_Z1C3A29C9(defaultCwlVersion))))), fields_2));
+      return YAMLElement_Object(cons(YAMLElement_Mapping(YAMLContent_create_Z1C3A29C9("cwlVersion"), YAMLElement_Object(singleton(YAMLElement_Value(YAMLContent_create_Z1C3A29C9(defaultCwlVersion))))), fields_2));
     }
   } else {
     return yamlElement;
   }
 }
-function Decode_workflowStepRunDecoder(defaultCwlVersion, runValue) {
+function Decode_workflowStepRunDecoder(warnings, defaultCwlVersion, runValue) {
   let matchResult, v;
   switch (runValue.tag) {
     case /* Object */
@@ -2201,7 +2553,7 @@ function Decode_workflowStepRunDecoder(defaultCwlVersion, runValue) {
     case 0:
       return WorkflowStepRun_RunString(v.Value);
     case 1: {
-      const matchValue = Decode_decodeCWLProcessingUnitElement(Decode_withDefaultCwlVersion(defaultCwlVersion, runValue));
+      const matchValue = Decode_decodeCWLProcessingUnitElementWithWarnings(warnings, Decode_withDefaultCwlVersion(defaultCwlVersion, runValue));
       switch (matchValue.tag) {
         case /* Workflow */
         1:
@@ -2220,14 +2572,17 @@ function Decode_workflowStepRunDecoder(defaultCwlVersion, runValue) {
       throw new Error(toText(interpolate("Unsupported run value for workflow step: %A%P()", [runValue])));
   }
 }
-function Decode_decodeWorkflowStepFromValueWithId(defaultCwlVersion, stepId, value) {
-  const run = Decode_workflowStepRunDecoder(defaultCwlVersion, object((get$0027) => {
+function Decode_decodeWorkflowStepFromValueWithId(warnings, defaultCwlVersion, path, stepId, value) {
+  const run = Decode_workflowStepRunDecoder(warnings, defaultCwlVersion, object((get$0027) => {
     const objectArg = get$0027.Required;
     return objectArg.Field("run", (x) => x);
   }, value));
   const inputs = object((get$0027_1) => {
+    let arg_3;
+    const path_1 = `${path}.in`;
+    arg_3 = (value_1) => Decode_inputStepDecoderWithWarnings(warnings, path_1, value_1);
     const objectArg_1 = get$0027_1.Required;
-    return objectArg_1.Field("in", Decode_inputStepDecoder);
+    return objectArg_1.Field("in", arg_3);
   }, value);
   const outputs = Decode_outputStepsDecoder(value);
   const requirements = Decode_requirementsDecoder(value);
@@ -2240,12 +2595,26 @@ function Decode_decodeWorkflowStepFromValueWithId(defaultCwlVersion, stepId, val
   if (hints != null) {
     wfStep.Hints = hints;
   }
+  Decode_overflowIntoDynamicObj(wfStep, toList(WorkflowStep.KnownFieldNames), value);
   return wfStep;
 }
 function Decode_decodeWorkflowStepFromArrayItem(defaultCwlVersion, item) {
-  return Decode_decodeWorkflowStepFromValueWithId(defaultCwlVersion, Decode_stringFieldDecoder("id")(item), item);
+  return Decode_decodeWorkflowStepFromValueWithId(void 0, defaultCwlVersion, "steps[]", Decode_stringFieldDecoder("id")(item), item);
+}
+function Decode_decodeWorkflowStepFromArrayItemWithWarnings(warnings, defaultCwlVersion, index, item) {
+  const matchValue = Decode_tryGetStringField("id", item);
+  if (matchValue == null) {
+    if (Decode_isIgnorableYamlNoise(item)) {
+      return void 0;
+    } else {
+      Decode_addWarning(warnings, `steps[${index}]`, "Skipped malformed unnamed CWL workflow step entry.", item);
+      return void 0;
+    }
+  } else {
+    return Decode_decodeWorkflowStepFromValueWithId(warnings, defaultCwlVersion, `steps[${index}]`, value(matchValue), item);
+  }
 }
-function Decode_stepArrayDecoderWithVersion(defaultCwlVersion, value) {
+function Decode_stepArrayDecoderWithVersion(warnings, defaultCwlVersion, value) {
   let matchResult, items;
   switch (value.tag) {
     case /* Object */
@@ -2278,38 +2647,37 @@ function Decode_stepArrayDecoderWithVersion(defaultCwlVersion, value) {
   }
   switch (matchResult) {
     case 0: {
-      const collection = map((item) => Decode_decodeWorkflowStepFromArrayItem(defaultCwlVersion, item), items);
+      const collection = choose((x) => x, mapIndexed((index, item) => Decode_decodeWorkflowStepFromArrayItemWithWarnings(warnings, defaultCwlVersion, index, item), items));
       return Array.from(collection);
     }
     default: {
       const dict = object((get$) => get$.Overflow.FieldList(empty()), value);
-      const collection_1 = toArray(delay(() => map$2((key) => Decode_decodeWorkflowStepFromValueWithId(defaultCwlVersion, key, getItemFromDict(dict, key)), dict.keys())));
+      const collection_1 = toArray(delay(() => map$2((key) => Decode_decodeWorkflowStepFromValueWithId(warnings, defaultCwlVersion, `steps.${key}`, key, getItemFromDict(dict, key)), dict.keys())));
       return Array.from(collection_1);
     }
   }
 }
-function Decode_stepsDecoderWithVersion(defaultCwlVersion) {
+function Decode_stepsDecoderWithVersion(warnings, defaultCwlVersion) {
   return (value_1) => object((get$) => {
     const objectArg = get$.Required;
-    return objectArg.Field("steps", (value) => Decode_stepArrayDecoderWithVersion(defaultCwlVersion, value));
+    return objectArg.Field("steps", (value) => Decode_stepArrayDecoderWithVersion(warnings, defaultCwlVersion, value));
   }, value_1);
 }
-function Decode_commandLineToolDecoder(yamlCWL) {
+function Decode_commandLineToolDecoder(warnings, yamlCWL) {
   const cwlVersion = Decode_versionDecoder(yamlCWL);
-  const outputs = Decode_outputsDecoder(yamlCWL);
-  const inputs = Decode_inputsDecoder(yamlCWL);
+  const outputs = Decode_outputsDecoderWithWarnings(warnings)(yamlCWL);
+  const inputs = Decode_inputsDecoderWithWarnings(warnings)(yamlCWL);
   const requirements = Decode_requirementsDecoder(yamlCWL);
   const hints = Decode_hintsDecoder(yamlCWL);
   const intent = Decode_intentDecoder(yamlCWL);
   const baseCommand = Decode_baseCommandDecoder(yamlCWL);
   const doc = Decode_docDecoder(yamlCWL);
   const label = Decode_labelDecoder(yamlCWL);
-  const description = new CWLToolDescription(outputs, cwlVersion, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(Decode_idDecoder(yamlCWL)));
+  const description = new CWLToolDescription(outputs, cwlVersion, void 0, unwrap(Decode_tryGetYamlField("arguments", yamlCWL)), unwrap(Decode_tryGetStringField("stdin", yamlCWL)), unwrap(Decode_tryGetStringField("stderr", yamlCWL)), unwrap(Decode_tryGetStringField("stdout", yamlCWL)), unwrap(Decode_tryGetIntArrayField("successCodes", yamlCWL)), unwrap(Decode_tryGetIntArrayField("temporaryFailCodes", yamlCWL)), unwrap(Decode_tryGetIntArrayField("permanentFailCodes", yamlCWL)), void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(Decode_idDecoder(yamlCWL)));
   let metadata;
   const md = new DynamicObj();
-  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "baseCommand", "arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
+  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(toList(CWLToolDescription.KnownFieldNames))), yamlCWL);
   metadata = md;
-  object((get$_1) => Decode_overflowDecoder(description, get$_1.MultipleOptional.FieldList(ofArray(["arguments", "stdin", "stderr", "stdout", "successCodes", "temporaryFailCodes", "permanentFailCodes"]))), yamlCWL);
   if (inputs != null) {
     description.Inputs = inputs;
   }
@@ -2336,10 +2704,10 @@ function Decode_commandLineToolDecoder(yamlCWL) {
   }
   return description;
 }
-function Decode_expressionToolDecoder(yamlCWL) {
+function Decode_expressionToolDecoder(warnings, yamlCWL) {
   const cwlVersion = Decode_versionDecoder(yamlCWL);
-  const outputs = Decode_outputsDecoder(yamlCWL);
-  const inputs = Decode_inputsDecoder(yamlCWL);
+  const outputs = Decode_outputsDecoderWithWarnings(warnings)(yamlCWL);
+  const inputs = Decode_inputsDecoderWithWarnings(warnings)(yamlCWL);
   const requirements = Decode_requirementsDecoder(yamlCWL);
   const hints = Decode_hintsDecoder(yamlCWL);
   const intent = Decode_intentDecoder(yamlCWL);
@@ -2351,7 +2719,7 @@ function Decode_expressionToolDecoder(yamlCWL) {
   }, yamlCWL), cwlVersion, void 0, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(Decode_idDecoder(yamlCWL)));
   let metadata;
   const md = new DynamicObj();
-  object((get$_1) => Decode_overflowDecoder(md, get$_1.Overflow.FieldList(ofArray(["inputs", "outputs", "class", "id", "label", "doc", "intent", "requirements", "hints", "cwlVersion", "expression"]))), yamlCWL);
+  object((get$_1) => Decode_overflowDecoder(md, get$_1.Overflow.FieldList(toList(CWLExpressionToolDescription.KnownFieldNames))), yamlCWL);
   metadata = md;
   if (inputs != null) {
     description.Inputs = inputs;
@@ -2376,11 +2744,11 @@ function Decode_expressionToolDecoder(yamlCWL) {
   }
   return description;
 }
-function Decode_operationDecoder(yamlCWL) {
+function Decode_operationDecoder(warnings, yamlCWL) {
   const cwlVersion = Decode_versionDecoder(yamlCWL);
-  const outputs = Decode_outputsDecoder(yamlCWL);
+  const outputs = Decode_outputsDecoderWithWarnings(warnings)(yamlCWL);
   let inputs;
-  const matchValue = Decode_inputsDecoder(yamlCWL);
+  const matchValue = Decode_inputsDecoderWithWarnings(warnings)(yamlCWL);
   if (matchValue == null) {
     throw new Error("Inputs are required for an operation");
   } else {
@@ -2394,7 +2762,7 @@ function Decode_operationDecoder(yamlCWL) {
   const description = new CWLOperationDescription(inputs, outputs, cwlVersion, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(Decode_idDecoder(yamlCWL)));
   let metadata;
   const md = new DynamicObj();
-  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "label", "doc", "intent", "class", "id", "requirements", "hints", "cwlVersion"]))), yamlCWL);
+  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(toList(CWLOperationDescription.KnownFieldNames))), yamlCWL);
   metadata = md;
   if (requirements != null) {
     description.Requirements = requirements;
@@ -2416,11 +2784,11 @@ function Decode_operationDecoder(yamlCWL) {
   }
   return description;
 }
-function Decode_workflowDecoder(yamlCWL) {
+function Decode_workflowDecoder(warnings, yamlCWL) {
   const cwlVersion = Decode_versionDecoder(yamlCWL);
-  const outputs = Decode_outputsDecoder(yamlCWL);
+  const outputs = Decode_outputsDecoderWithWarnings(warnings)(yamlCWL);
   let inputs;
-  const matchValue = Decode_inputsDecoder(yamlCWL);
+  const matchValue = Decode_inputsDecoderWithWarnings(warnings)(yamlCWL);
   if (matchValue == null) {
     throw new Error("Inputs are required for a workflow");
   } else {
@@ -2429,13 +2797,13 @@ function Decode_workflowDecoder(yamlCWL) {
   const requirements = Decode_requirementsDecoder(yamlCWL);
   const hints = Decode_hintsDecoder(yamlCWL);
   const intent = Decode_intentDecoder(yamlCWL);
-  const steps = Decode_stepsDecoderWithVersion(cwlVersion)(yamlCWL);
+  const steps = Decode_stepsDecoderWithVersion(warnings, cwlVersion)(yamlCWL);
   const doc = Decode_docDecoder(yamlCWL);
   const label = Decode_labelDecoder(yamlCWL);
   const description = new CWLWorkflowDescription(steps, inputs, outputs, cwlVersion, void 0, void 0, void 0, void 0, void 0, void 0, unwrap(Decode_idDecoder(yamlCWL)));
   let metadata;
   const md = new DynamicObj();
-  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(ofArray(["inputs", "outputs", "label", "doc", "intent", "class", "steps", "id", "requirements", "hints", "cwlVersion"]))), yamlCWL);
+  object((get$) => Decode_overflowDecoder(md, get$.Overflow.FieldList(toList(CWLWorkflowDescription.KnownFieldNames))), yamlCWL);
   metadata = md;
   if (requirements != null) {
     description.Requirements = requirements;
@@ -2457,243 +2825,218 @@ function Decode_workflowDecoder(yamlCWL) {
   }
   return description;
 }
-function Decode_decodeCWLProcessingUnitElement(yamlCWL) {
+function Decode_decodeCWLProcessingUnitElementWithWarnings(warnings, yamlCWL) {
   const cls = Decode_classDecoder(yamlCWL);
   switch (cls) {
     case "CommandLineTool":
-      return CWLProcessingUnit_CommandLineTool(Decode_commandLineToolDecoder(yamlCWL));
+      return CWLProcessingUnit_CommandLineTool(Decode_commandLineToolDecoder(warnings, yamlCWL));
     case "Workflow":
-      return CWLProcessingUnit_Workflow(Decode_workflowDecoder(yamlCWL));
+      return CWLProcessingUnit_Workflow(Decode_workflowDecoder(warnings, yamlCWL));
     case "ExpressionTool":
-      return CWLProcessingUnit_ExpressionTool(Decode_expressionToolDecoder(yamlCWL));
+      return CWLProcessingUnit_ExpressionTool(Decode_expressionToolDecoder(warnings, yamlCWL));
     case "Operation":
-      return CWLProcessingUnit_Operation(Decode_operationDecoder(yamlCWL));
+      return CWLProcessingUnit_Operation(Decode_operationDecoder(warnings, yamlCWL));
     default:
       throw new Error(`Invalid or unsupported CWL class: ${cls}`);
   }
 }
-const Decode_stepArrayDecoder = (value) => Decode_stepArrayDecoderWithVersion("v1.2", value);
-const Decode_stepsDecoder = Decode_stepsDecoderWithVersion("v1.2");
+function Decode_decodeCWLProcessingUnitElement(yamlCWL) {
+  return Decode_decodeCWLProcessingUnitElementWithWarnings(void 0, yamlCWL);
+}
+const Decode_stepArrayDecoder = (value) => Decode_stepArrayDecoderWithVersion(void 0, "v1.2", value);
+const Decode_stepsDecoder = Decode_stepsDecoderWithVersion(void 0, "v1.2");
+function Decode_decodeCommandLineToolWithWarnings(cwl) {
+  const warnings = [];
+  return new Decode_DecodeResult$1(Decode_commandLineToolDecoder(warnings, Decode_readSanitizedYaml(cwl)), warnings);
+}
 function Decode_decodeCommandLineTool(cwl) {
-  return Decode_commandLineToolDecoder(Decode_readSanitizedYaml(cwl));
+  return Decode_decodeCommandLineToolWithWarnings(cwl).Value;
+}
+function Decode_decodeWorkflowWithWarnings(cwl) {
+  const warnings = [];
+  return new Decode_DecodeResult$1(Decode_workflowDecoder(warnings, Decode_readSanitizedYaml(cwl)), warnings);
 }
 function Decode_decodeWorkflow(cwl) {
-  return Decode_workflowDecoder(Decode_readSanitizedYaml(cwl));
+  return Decode_decodeWorkflowWithWarnings(cwl).Value;
+}
+function Decode_decodeExpressionToolWithWarnings(cwl) {
+  const warnings = [];
+  return new Decode_DecodeResult$1(Decode_expressionToolDecoder(warnings, Decode_readSanitizedYaml(cwl)), warnings);
 }
 function Decode_decodeExpressionTool(cwl) {
-  return Decode_expressionToolDecoder(Decode_readSanitizedYaml(cwl));
+  return Decode_decodeExpressionToolWithWarnings(cwl).Value;
+}
+function Decode_decodeOperationWithWarnings(cwl) {
+  const warnings = [];
+  return new Decode_DecodeResult$1(Decode_operationDecoder(warnings, Decode_readSanitizedYaml(cwl)), warnings);
 }
 function Decode_decodeOperation(cwl) {
-  return Decode_operationDecoder(Decode_readSanitizedYaml(cwl));
+  return Decode_decodeOperationWithWarnings(cwl).Value;
+}
+function Decode_decodeCWLProcessingUnitWithWarnings(cwl) {
+  const warnings = [];
+  return new Decode_DecodeResult$1(Decode_decodeCWLProcessingUnitElementWithWarnings(warnings, Decode_readSanitizedYaml(cwl)), warnings);
 }
 function Decode_decodeCWLProcessingUnit(cwl) {
-  return Decode_decodeCWLProcessingUnitElement(Decode_readSanitizedYaml(cwl));
+  return Decode_decodeCWLProcessingUnitWithWarnings(cwl).Value;
 }
 function DecodeParameters_cwlParameterReferenceDecoder(get$, key, yEle) {
-  let v_1;
-  let matchResult, v, v1, v2, s;
-  if (yEle.tag === /* Object */
-  3) {
-    if (!isEmpty(yEle.fields[0])) {
-      switch (head(yEle.fields[0]).tag) {
-        case /* Value */
-        1: {
-          if (isEmpty(tail(yEle.fields[0]))) {
-            matchResult = 0;
-            v = head(yEle.fields[0]).fields[0];
+  let collection, collection_1, className_2, matchValue_4, sequenceValue, scalarOrObject, matchValue_5;
+  const tryScalarString = (_arg) => {
+    let matchResult, v;
+    switch (_arg.tag) {
+      case /* Value */
+      1: {
+        matchResult = 0;
+        v = _arg.fields[0];
+        break;
+      }
+      case /* Object */
+      3: {
+        if (!isEmpty(_arg.fields[0])) {
+          if (head(_arg.fields[0]).tag === /* Value */
+          1) {
+            if (isEmpty(tail(_arg.fields[0]))) {
+              matchResult = 0;
+              v = head(_arg.fields[0]).fields[0];
+            } else {
+              matchResult = 1;
+            }
           } else {
-            matchResult = 3;
+            matchResult = 1;
           }
-          break;
+        } else {
+          matchResult = 1;
         }
-        case /* Mapping */
-        0: {
-          if (head(yEle.fields[0]).fields[1].tag === /* Object */
-          3) {
-            if (!isEmpty(head(yEle.fields[0]).fields[1].fields[0])) {
-              if (head(head(yEle.fields[0]).fields[1].fields[0]).tag === /* Value */
-              1) {
-                if (isEmpty(tail(head(yEle.fields[0]).fields[1].fields[0]))) {
-                  if (!isEmpty(tail(yEle.fields[0]))) {
-                    if (head(tail(yEle.fields[0])).tag === /* Mapping */
-                    0) {
-                      if (head(tail(yEle.fields[0])).fields[1].tag === /* Object */
-                      3) {
-                        if (!isEmpty(head(tail(yEle.fields[0])).fields[1].fields[0])) {
-                          if (head(head(tail(yEle.fields[0])).fields[1].fields[0]).tag === /* Value */
-                          1) {
-                            if (isEmpty(tail(head(tail(yEle.fields[0])).fields[1].fields[0]))) {
-                              if (isEmpty(tail(tail(yEle.fields[0])))) {
-                                matchResult = 1;
-                                v1 = head(head(yEle.fields[0]).fields[1].fields[0]).fields[0];
-                                v2 = head(head(tail(yEle.fields[0])).fields[1].fields[0]).fields[0];
-                              } else {
-                                matchResult = 3;
-                              }
-                            } else {
-                              matchResult = 3;
-                            }
-                          } else {
-                            matchResult = 3;
-                          }
-                        } else {
-                          matchResult = 3;
-                        }
-                      } else {
-                        matchResult = 3;
-                      }
-                    } else {
-                      matchResult = 3;
-                    }
-                  } else {
-                    matchResult = 3;
-                  }
-                } else {
-                  matchResult = 3;
-                }
-              } else {
-                matchResult = 3;
-              }
+        break;
+      }
+      default:
+        matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0:
+        return v.Value;
+      default:
+        return void 0;
+    }
+  };
+  const tryField = (fieldName, value) => {
+    try {
+      return object((get$_1) => {
+        const objectArg = get$_1.Optional;
+        return objectArg.Field(fieldName, (x) => x);
+      }, value);
+    } catch (matchValue) {
+      if (Decode_isRecoverableDecodingError(matchValue)) {
+        return void 0;
+      } else {
+        throw matchValue;
+      }
+    }
+  };
+  const tryStringField = (fieldName_1, value_1) => bind(tryScalarString, tryField(fieldName_1, value_1));
+  const withOverflow = (reference, value_2) => {
+    Decode_overflowIntoDynamicObj(reference, toList(CWLParameterReference.KnownFieldNames), value_2);
+    return reference;
+  };
+  const pathValue = (value_4) => orElseWith(tryStringField("path", value_4), () => tryStringField("location", value_4));
+  let matchResult_1, v_1, s;
+  switch (yEle.tag) {
+    case /* Value */
+    1: {
+      matchResult_1 = 0;
+      v_1 = yEle.fields[0];
+      break;
+    }
+    case /* Object */
+    3: {
+      if (!isEmpty(yEle.fields[0])) {
+        switch (head(yEle.fields[0]).tag) {
+          case /* Value */
+          1: {
+            if (isEmpty(tail(yEle.fields[0]))) {
+              matchResult_1 = 0;
+              v_1 = head(yEle.fields[0]).fields[0];
             } else {
-              matchResult = 3;
+              matchResult_1 = 2;
             }
-          } else {
-            matchResult = 3;
+            break;
           }
-          break;
-        }
-        case /* Sequence */
-        2: {
-          if (isEmpty(tail(yEle.fields[0]))) {
-            matchResult = 2;
-            s = head(yEle.fields[0]).fields[0];
-          } else {
-            matchResult = 3;
+          case /* Sequence */
+          2: {
+            if (isEmpty(tail(yEle.fields[0]))) {
+              matchResult_1 = 1;
+              s = head(yEle.fields[0]).fields[0];
+            } else {
+              matchResult_1 = 2;
+            }
+            break;
           }
-          break;
+          default:
+            matchResult_1 = 2;
         }
-        default:
-          matchResult = 3;
+      } else {
+        matchResult_1 = 2;
       }
-    } else {
-      matchResult = 3;
+      break;
     }
-  } else {
-    matchResult = 3;
+    case /* Sequence */
+    2: {
+      matchResult_1 = 1;
+      s = yEle.fields[0];
+      break;
+    }
+    default:
+      matchResult_1 = 3;
   }
-  switch (matchResult) {
+  switch (matchResult_1) {
     case 0:
-      return new CWLParameterReference(key, [v.Value]);
-    case 1:
-      return new CWLParameterReference(key, [v2.Value], Decode_cwlTypeStringMatcher(v1.Value, get$)[0]);
+      return new CWLParameterReference(key, [v_1.Value]);
+    case 1: {
+      const items = s;
+      const matchValue_6 = tryHead(items);
+      if (matchValue_6 == null) {
+        return new CWLParameterReference(key, []);
+      } else {
+        const matchValue_7 = tryStringField("class", value(matchValue_6));
+        let matchResult_2, className_3;
+        if (matchValue_7 != null) {
+          if (className_2 = value(matchValue_7), className_2 === "File" ? true : className_2 === "Directory") {
+            matchResult_2 = 0;
+            className_3 = value(matchValue_7);
+          } else {
+            matchResult_2 = 1;
+          }
+        } else {
+          matchResult_2 = 1;
+        }
+        switch (matchResult_2) {
+          case 0:
+            return new CWLParameterReference(key, (collection = choose(pathValue, items), Array.from(collection)), CWLType_Array(new InputArraySchema(className_3 === "Directory" ? CWLType_Directory(new DirectoryInstance()) : CWLType_File(new FileInstance()))));
+          default:
+            return new CWLParameterReference(key, (collection_1 = choose(tryScalarString, items), Array.from(collection_1)));
+        }
+      }
+    }
     case 2: {
-      const matchValue = tryHead(s);
-      let matchResult_1, mappings;
-      if (matchValue != null) {
-        if (value(matchValue).tag === /* Object */
-        3) {
-          matchResult_1 = 0;
-          mappings = value(matchValue).fields[0];
+      const value_5 = yEle;
+      const matchValue_1 = tryStringField("class", value_5);
+      const matchValue_2 = tryStringField("type", value_5);
+      if (matchValue_1 == null) {
+        if (matchValue_2 == null) {
+          return withOverflow(new CWLParameterReference(key, []), value_5);
         } else {
-          matchResult_1 = 1;
+          const patternInput = Decode_cwlTypeStringMatcher(value(matchValue_2), get$);
+          return withOverflow(new CWLParameterReference(key, (matchValue_4 = tryField("value", value_5), matchValue_4 == null ? [] : value(matchValue_4).tag === /* Object */
+          3 ? !isEmpty(value(matchValue_4).fields[0]) ? head(value(matchValue_4).fields[0]).tag === /* Sequence */
+          2 ? isEmpty(tail(value(matchValue_4).fields[0])) ? (sequenceValue = value(matchValue_4), resizearray(string, sequenceValue)) : (scalarOrObject = value(matchValue_4), matchValue_5 = tryScalarString(scalarOrObject), matchValue_5 == null ? [] : [value(matchValue_5)]) : (scalarOrObject = value(matchValue_4), matchValue_5 = tryScalarString(scalarOrObject), matchValue_5 == null ? [] : [value(matchValue_5)]) : (scalarOrObject = value(matchValue_4), matchValue_5 = tryScalarString(scalarOrObject), matchValue_5 == null ? [] : [value(matchValue_5)]) : value(matchValue_4).tag === /* Sequence */
+          2 ? (sequenceValue = value(matchValue_4), resizearray(string, sequenceValue)) : (scalarOrObject = value(matchValue_4), matchValue_5 = tryScalarString(scalarOrObject), matchValue_5 == null ? [] : [value(matchValue_5)])), patternInput[0]), value_5);
         }
       } else {
-        matchResult_1 = 1;
-      }
-      switch (matchResult_1) {
-        case 0:
-          if (!exists((_arg) => {
-            if (_arg.tag === /* Mapping */
-            0) {
-              return true;
-            } else {
-              return false;
-            }
-          }, mappings)) {
-            return new CWLParameterReference(key, resizearray(string, YAMLElement_Sequence(s)));
-          } else if (exists((_arg_1) => {
-            let matchResult_2, k_1;
-            if (_arg_1.tag === /* Mapping */
-            0) {
-              if (_arg_1.fields[0].Value === "class") {
-                matchResult_2 = 0;
-                k_1 = _arg_1.fields[0];
-              } else {
-                matchResult_2 = 1;
-              }
-            } else {
-              matchResult_2 = 1;
-            }
-            switch (matchResult_2) {
-              case 0:
-                return true;
-              default:
-                return false;
-            }
-          }, mappings)) {
-            const paths = [];
-            const enumerator = getEnumerator(s);
-            try {
-              while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
-                const item = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                if (item.tag === /* Object */
-                3) {
-                  const enumerator_1 = getEnumerator(item.fields[0]);
-                  try {
-                    while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
-                      const mapping = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
-                      let matchResult_3, k_3, v_2;
-                      if (mapping.tag === /* Mapping */
-                      0) {
-                        if (mapping.fields[1].tag === /* Object */
-                        3) {
-                          if (!isEmpty(mapping.fields[1].fields[0])) {
-                            if (head(mapping.fields[1].fields[0]).tag === /* Value */
-                            1) {
-                              if (isEmpty(tail(mapping.fields[1].fields[0]))) {
-                                if (v_1 = head(mapping.fields[1].fields[0]).fields[0], mapping.fields[0].Value === "path") {
-                                  matchResult_3 = 0;
-                                  k_3 = mapping.fields[0];
-                                  v_2 = head(mapping.fields[1].fields[0]).fields[0];
-                                } else {
-                                  matchResult_3 = 1;
-                                }
-                              } else {
-                                matchResult_3 = 1;
-                              }
-                            } else {
-                              matchResult_3 = 1;
-                            }
-                          } else {
-                            matchResult_3 = 1;
-                          }
-                        } else {
-                          matchResult_3 = 1;
-                        }
-                      } else {
-                        matchResult_3 = 1;
-                      }
-                      switch (matchResult_3) {
-                        case 0: {
-                          void paths.push(v_2.Value);
-                          break;
-                        }
-                      }
-                    }
-                  } finally {
-                    disposeSafe(enumerator_1);
-                  }
-                }
-              }
-            } finally {
-              disposeSafe(enumerator);
-            }
-            return new CWLParameterReference(key, paths, CWLType_Array(new InputArraySchema(CWLType_File(FileInstance_$ctor()), void 0, void 0, void 0)));
-          } else {
-            return new CWLParameterReference(key, []);
-          }
-        default:
-          return new CWLParameterReference(key, resizearray(string, YAMLElement_Sequence(s)));
+        let cwlType;
+        const className = value(matchValue_1);
+        cwlType = className === "File" ? CWLType_file() : className === "Directory" ? CWLType_directory() : void 0;
+        return withOverflow(new CWLParameterReference(key, defaultArg(map((p) => [p], pathValue(value_5)), []), unwrap(cwlType)), value_5);
       }
     }
     default:
@@ -2709,4 +3052,4 @@ function DecodeParameters_decodeYAMLParameterFile(yaml) {
   return DecodeParameters_cwlparameterReferenceArrayDecoder(read(yaml));
 }
 
-export { DecodeParameters_cwlParameterReferenceDecoder, DecodeParameters_cwlparameterReferenceArrayDecoder, DecodeParameters_decodeYAMLParameterFile, Decode_baseCommandDecoder, Decode_boolOptionFieldDecoder, Decode_classDecoder, Decode_commandLineToolDecoder, Decode_countLeadingSpaces, Decode_cwlSimpleTypeFromString, Decode_cwlTypeDecoder, Decode_cwlTypeDecoder$0027, Decode_cwlTypeStringMatcher, Decode_decodeCWLProcessingUnit, Decode_decodeCWLProcessingUnitElement, Decode_decodeCommandLineTool, Decode_decodeExpressionTool, Decode_decodeHintElement, Decode_decodeOperation, Decode_decodeResourceScalar, Decode_decodeSchemaSaladString, Decode_decodeStepInputFromArrayItem, Decode_decodeStepInputFromValue, Decode_decodeStepInputsFromArray, Decode_decodeStepInputsFromMap, Decode_decodeStepOutputItem, Decode_decodeStringArrayOrScalar, Decode_decodeStringOrExpression, Decode_decodeWorkflow, Decode_decodeWorkflowStepFromArrayItem, Decode_decodeWorkflowStepFromValueWithId, Decode_direntDecoder, Decode_docDecoder, Decode_dockerRequirementDecoder, Decode_envVarRequirementDecoder, Decode_expressionStringOptionFieldDecoder, Decode_expressionToolDecoder, Decode_hasField, Decode_hintArrayDecoder, Decode_hintsDecoder, Decode_idDecoder, Decode_initialWorkDirEntryDecoder, Decode_initialWorkDirRequirementDecoder, Decode_inlineJavascriptRequirementDecoder, Decode_inplaceUpdateRequirementDecoder, Decode_inputArrayDecoder, Decode_inputArraySchemaDecoder, Decode_inputBindingDecoder, Decode_inputEnumSchemaDecoder, Decode_inputRecordFieldDecoder, Decode_inputRecordSchemaDecoder, Decode_inputStepDecoder, Decode_inputsDecoder, Decode_intentDecoder, Decode_isBlankLine, Decode_isRecoverableDecodingError, Decode_labelDecoder, Decode_linkMergeFieldDecoder, Decode_loadListingRequirementDecoder, Decode_networkAccessRequirementDecoder, Decode_normalizeLineEndings, Decode_normalizeYamlInput, Decode_operationDecoder, Decode_optionalResourceField, Decode_outputArrayDecoder, Decode_outputBindingDecoder, Decode_outputBindingGlobDecoder, Decode_outputSourceDecoder, Decode_outputStepsDecoder, Decode_outputsDecoder, Decode_overflowDecoder, Decode_parseArrayShorthand, Decode_pickValueFieldDecoder, Decode_readSanitizedYaml, Decode_removeFullLineComments, Decode_removeYamlComments, Decode_requirementArrayDecoder, Decode_requirementFromTypeName, Decode_requirementsDecoder, Decode_resourceRequirementDecoder, Decode_scatterFieldDecoder, Decode_scatterMethodFieldDecoder, Decode_schemaDefRequirementDecoder, Decode_schemaDefRequirementTypeDecoder, Decode_softwareRequirementDecoder, Decode_sourceArrayFieldDecoder, Decode_stepArrayDecoder, Decode_stepArrayDecoderWithVersion, Decode_stepsDecoder, Decode_stepsDecoderWithVersion, Decode_stringFieldDecoder, Decode_stringOptionFieldDecoder, Decode_stringOrStringArrayDecoder, Decode_stripLeadingShebang, Decode_toolTimeLimitRequirementDecoder, Decode_tryDecodeBoolScalar, Decode_tryDecodeFieldsAsArray, Decode_tryDecodeFieldsAsMap, Decode_tryDecodeKnownRequirementFromElement, Decode_tryParseBlockScalarHeader, Decode_versionDecoder, Decode_withDefaultCwlVersion, Decode_workReuseRequirementDecoder, Decode_workflowDecoder, Decode_workflowStepRunDecoder, Decode_yamlElementOptionFieldDecoder, ResizeArray_map, inputArraySchemaDecoder$0040324, inputArraySchemaDecoder$0040324$002D1, inputEnumSchemaDecoder$0040404, inputEnumSchemaDecoder$0040404$002D1, inputRecordFieldDecoder$0040338, inputRecordFieldDecoder$0040338$002D1, inputRecordSchemaDecoder$0040377, inputRecordSchemaDecoder$0040377$002D1 };
+export { DecodeParameters_cwlParameterReferenceDecoder, DecodeParameters_cwlparameterReferenceArrayDecoder, DecodeParameters_decodeYAMLParameterFile, Decode_DecodeResult$1, Decode_DecodeResult$1_$reflection, Decode_DecodeWarning, Decode_DecodeWarning_$reflection, Decode_addRequirementPayloadOverflow, Decode_addWarning, Decode_baseCommandDecoder, Decode_boolOptionFieldDecoder, Decode_boxOverflowInt64, Decode_classDecoder, Decode_commandLineToolDecoder, Decode_cwlSimpleTypeFromString, Decode_cwlTypeDecoder, Decode_cwlTypeDecoder$0027, Decode_cwlTypeStringMatcher, Decode_decodeCWLProcessingUnit, Decode_decodeCWLProcessingUnitElement, Decode_decodeCWLProcessingUnitElementWithWarnings, Decode_decodeCWLProcessingUnitWithWarnings, Decode_decodeCommandLineTool, Decode_decodeCommandLineToolWithWarnings, Decode_decodeDirectoryInstanceFields, Decode_decodeExpressionTool, Decode_decodeExpressionToolWithWarnings, Decode_decodeFileInstanceFields, Decode_decodeHintElement, Decode_decodeInputSequenceItem, Decode_decodeNamedInput, Decode_decodeNamedOutput, Decode_decodeOperation, Decode_decodeOperationWithWarnings, Decode_decodeOutputSequenceItem, Decode_decodeResourceScalar, Decode_decodeSchemaSaladString, Decode_decodeStepInputFromArrayItem, Decode_decodeStepInputFromValue, Decode_decodeStepInputsFromArray, Decode_decodeStepInputsFromArrayWithWarnings, Decode_decodeStepInputsFromMap, Decode_decodeStepOutputItem, Decode_decodeStringArrayOrScalar, Decode_decodeStringOrExpression, Decode_decodeWorkflow, Decode_decodeWorkflowStepFromArrayItem, Decode_decodeWorkflowStepFromArrayItemWithWarnings, Decode_decodeWorkflowStepFromValueWithId, Decode_decodeWorkflowWithWarnings, Decode_direntDecoder, Decode_docDecoder, Decode_dockerRequirementDecoder, Decode_envVarRequirementDecoder, Decode_expressionStringOptionFieldDecoder, Decode_expressionToolDecoder, Decode_hasField, Decode_hintArrayDecoder, Decode_hintsDecoder, Decode_idDecoder, Decode_initialWorkDirEntryDecoder, Decode_initialWorkDirRequirementDecoder, Decode_inlineJavascriptRequirementDecoder, Decode_inplaceUpdateRequirementDecoder, Decode_inputArrayDecoder, Decode_inputArrayDecoderWithWarnings, Decode_inputArraySchemaDecoder, Decode_inputBindingDecoder, Decode_inputEnumSchemaDecoder, Decode_inputRecordFieldDecoder, Decode_inputRecordSchemaDecoder, Decode_inputStepDecoder, Decode_inputStepDecoderWithWarnings, Decode_inputsDecoder, Decode_inputsDecoderWithWarnings, Decode_intentDecoder, Decode_isIgnorableYamlNoise, Decode_isRecoverableDecodingError, Decode_labelDecoder, Decode_linkMergeFieldDecoder, Decode_loadListingRequirementDecoder, Decode_networkAccessRequirementDecoder, Decode_operationDecoder, Decode_optionalResourceField, Decode_outputArrayDecoder, Decode_outputArrayDecoderWithWarnings, Decode_outputBindingDecoder, Decode_outputBindingGlobDecoder, Decode_outputSourceDecoder, Decode_outputStepsDecoder, Decode_outputsDecoder, Decode_outputsDecoderWithWarnings, Decode_overflowDecoder, Decode_overflowIntoDynamicObj, Decode_parseArrayShorthand, Decode_pickValueFieldDecoder, Decode_readSanitizedYaml, Decode_removeYamlComments, Decode_requirementArrayDecoder, Decode_requirementFromTypeName, Decode_requirementsDecoder, Decode_resourceRequirementDecoder, Decode_scatterFieldDecoder, Decode_scatterMethodFieldDecoder, Decode_schemaDefRequirementDecoder, Decode_schemaDefRequirementTypeDecoder, Decode_softwareRequirementDecoder, Decode_sourceArrayFieldDecoder, Decode_stepArrayDecoder, Decode_stepArrayDecoderWithVersion, Decode_stepsDecoder, Decode_stepsDecoderWithVersion, Decode_stringFieldDecoder, Decode_stringOptionFieldDecoder, Decode_stringOrStringArrayDecoder, Decode_toolTimeLimitRequirementDecoder, Decode_tryDecodeBoolScalar, Decode_tryDecodeFieldsAsArray, Decode_tryDecodeFieldsAsMap, Decode_tryDecodeKnownRequirementFromElement, Decode_tryGetBoolField, Decode_tryGetInt64Field, Decode_tryGetIntArrayField, Decode_tryGetLoadListingField, Decode_tryGetPresentField, Decode_tryGetStringField, Decode_tryGetYamlField, Decode_versionDecoder, Decode_withDefaultCwlVersion, Decode_workReuseRequirementDecoder, Decode_workflowDecoder, Decode_workflowStepRunDecoder, Decode_yamlElementOptionFieldDecoder, ResizeArray_map };