add nextflow d30e48d

2026-04-29 23:01:54 +02:00
parent d0b12d668d
commit 97cc9058d3
2840 changed files with 730250 additions and 0 deletions
--- a/nextflow/config/codenarc/codenarc.groovy
+++ b/nextflow/config/codenarc/codenarc.groovy
@@ -0,0 +1,351 @@
+/*
+ * Copyright 2013-2026, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+ruleset {
+
+    description '''
+        A Sample Groovy RuleSet containing all CodeNarc Rules, grouped by category.
+        You can use this as a template for your own custom RuleSet.
+        Just delete the rules that you don't want to include.
+        '''
+
+    // rulesets/basic.xml
+    AssertWithinFinallyBlock
+    AssignmentInConditional
+    BigDecimalInstantiation
+    BitwiseOperatorInConditional
+    BooleanGetBoolean
+    BrokenNullCheck
+    BrokenOddnessCheck
+    ClassForName
+    ComparisonOfTwoConstants
+    ComparisonWithSelf
+    ConstantAssertExpression
+    ConstantIfExpression
+    ConstantTernaryExpression
+    DeadCode
+    DoubleNegative
+    DuplicateCaseStatement
+    DuplicateMapKey
+    DuplicateSetValue
+    EmptyCatchBlock
+    EmptyElseBlock
+    EmptyFinallyBlock
+    EmptyForStatement
+    EmptyIfStatement
+    EmptyInstanceInitializer
+    EmptyMethod
+    EmptyStaticInitializer
+    EmptySwitchStatement
+    EmptySynchronizedStatement
+    EmptyTryBlock
+    EmptyWhileStatement
+    EqualsAndHashCode
+    EqualsOverloaded
+    ExplicitGarbageCollection
+    ForLoopShouldBeWhileLoop
+    HardCodedWindowsFileSeparator
+    HardCodedWindowsRootDirectory
+    IntegerGetInteger
+    RandomDoubleCoercedToZero
+    RemoveAllOnSelf
+    ReturnFromFinallyBlock
+    ThrowExceptionFromFinallyBlock
+
+    // rulesets/braces.xml
+    //ElseBlockBraces
+    ForStatementBraces
+    //IfStatementBraces
+    //WhileStatementBraces
+
+    // rulesets/concurrency.xml
+    BusyWait
+    DoubleCheckedLocking
+    InconsistentPropertyLocking
+    InconsistentPropertySynchronization
+    NestedSynchronization
+    StaticCalendarField
+    StaticConnection
+    StaticDateFormatField
+    StaticMatcherField
+    StaticSimpleDateFormatField
+    SynchronizedMethod
+    SynchronizedOnBoxedPrimitive
+    SynchronizedOnGetClass
+    SynchronizedOnReentrantLock
+    SynchronizedOnString
+    SynchronizedOnThis
+    SynchronizedReadObjectMethod
+    SystemRunFinalizersOnExit
+    ThreadGroup
+    ThreadLocalNotStaticFinal
+    ThreadYield
+    UseOfNotifyMethod
+    VolatileArrayField
+    VolatileLongOrDoubleField
+    WaitOutsideOfWhileLoop
+
+    // rulesets/convention.xml
+    ConfusingTernary
+    CouldBeElvis
+    HashtableIsObsolete
+    IfStatementCouldBeTernary
+    InvertedIfElse
+    LongLiteralWithLowerCaseL
+    ParameterReassignment
+    TernaryCouldBeElvis
+    VectorIsObsolete
+
+    // rulesets/design.xml
+    AbstractClassWithPublicConstructor
+    AbstractClassWithoutAbstractMethod
+    BooleanMethodReturnsNull
+    BuilderMethodWithSideEffects
+    CloneableWithoutClone
+    CloseWithoutCloseable
+    CompareToWithoutComparable
+    ConstantsOnlyInterface
+    EmptyMethodInAbstractClass
+    FinalClassWithProtectedMember
+    ImplementationAsType
+    PrivateFieldCouldBeFinal
+    PublicInstanceField
+    ReturnsNullInsteadOfEmptyArray
+    ReturnsNullInsteadOfEmptyCollection
+    SimpleDateFormatMissingLocale
+    StatelessSingleton
+
+    // rulesets/dry.xml
+    DuplicateListLiteral
+    DuplicateMapLiteral
+    DuplicateNumberLiteral
+    DuplicateStringLiteral
+
+    // rulesets/exceptions.xml
+    CatchArrayIndexOutOfBoundsException
+    CatchError
+    CatchException
+    CatchIllegalMonitorStateException
+    CatchIndexOutOfBoundsException
+    CatchNullPointerException
+    CatchRuntimeException
+    CatchThrowable
+    ConfusingClassNamedException
+    ExceptionExtendsError
+    ExceptionNotThrown
+    MissingNewInThrowStatement
+    ReturnNullFromCatchBlock
+    SwallowThreadDeath
+    ThrowError
+    ThrowException
+    ThrowNullPointerException
+    ThrowRuntimeException
+    ThrowThrowable
+
+    // rulesets/generic.xml
+    IllegalClassReference
+    IllegalPackageReference
+    IllegalRegex
+    RequiredRegex
+    RequiredString
+    StatelessClass
+
+    // rulesets/grails.xml
+    GrailsDomainHasEquals
+    GrailsDomainHasToString
+    GrailsDuplicateConstraint
+    GrailsDuplicateMapping
+    GrailsPublicControllerMethod
+    GrailsServletContextReference
+    GrailsSessionReference   // DEPRECATED
+    GrailsStatelessService
+
+    // rulesets/groovyism.xml
+    AssignCollectionSort
+    AssignCollectionUnique
+    ClosureAsLastMethodParameter
+    CollectAllIsDeprecated
+    ConfusingMultipleReturns
+    ExplicitArrayListInstantiation
+    ExplicitCallToAndMethod
+    ExplicitCallToCompareToMethod
+    ExplicitCallToDivMethod
+    ExplicitCallToEqualsMethod
+    ExplicitCallToGetAtMethod
+    ExplicitCallToLeftShiftMethod
+    ExplicitCallToMinusMethod
+    ExplicitCallToModMethod
+    ExplicitCallToMultiplyMethod
+    ExplicitCallToOrMethod
+    ExplicitCallToPlusMethod
+    ExplicitCallToPowerMethod
+    ExplicitCallToRightShiftMethod
+    ExplicitCallToXorMethod
+    ExplicitHashMapInstantiation
+    ExplicitHashSetInstantiation
+    ExplicitLinkedHashMapInstantiation
+    ExplicitLinkedListInstantiation
+    ExplicitStackInstantiation
+    ExplicitTreeSetInstantiation
+    GStringAsMapKey
+    GetterMethodCouldBeProperty
+    GroovyLangImmutable
+    UseCollectMany
+    UseCollectNested
+
+    // rulesets/imports.xml
+    DuplicateImport
+    ImportFromSamePackage
+    ImportFromSunPackages
+    MisorderedStaticImports
+    UnnecessaryGroovyImport
+    UnusedImport
+
+    // rulesets/jdbc.xml
+    DirectConnectionManagement
+    JdbcConnectionReference
+    JdbcResultSetReference
+    JdbcStatementReference
+
+    // rulesets/junit.xml
+    ChainedTest
+    CoupledTestCase
+    JUnitAssertAlwaysFails
+    JUnitAssertAlwaysSucceeds
+    JUnitFailWithoutMessage
+    JUnitLostTest
+    JUnitPublicNonTestMethod
+    JUnitSetUpCallsSuper
+    JUnitStyleAssertions
+    JUnitTearDownCallsSuper
+    JUnitTestMethodWithoutAssert
+    JUnitUnnecessarySetUp
+    JUnitUnnecessaryTearDown
+    JUnitUnnecessaryThrowsException
+    SpockIgnoreRestUsed
+    UnnecessaryFail
+    UseAssertEqualsInsteadOfAssertTrue
+    UseAssertFalseInsteadOfNegation
+    UseAssertNullInsteadOfAssertEquals
+    UseAssertSameInsteadOfAssertTrue
+    UseAssertTrueInsteadOfAssertEquals
+    UseAssertTrueInsteadOfNegation
+
+    // rulesets/logging.xml
+    LoggerForDifferentClass
+    LoggerWithWrongModifiers
+    LoggingSwallowsStacktrace
+    MultipleLoggers
+    PrintStackTrace
+    Println
+    SystemErrPrint
+    SystemOutPrint
+
+    // rulesets/naming.xml
+    AbstractClassName
+    ClassName
+    ConfusingMethodName
+    FactoryMethodName
+    FieldName
+    InterfaceName
+    MethodName
+    ObjectOverrideMisspelledMethodName
+    PackageName
+    ParameterName
+    PropertyName
+    //VariableName
+
+    // rulesets/security.xml
+    FileCreateTempFile
+    InsecureRandom
+    NonFinalPublicField
+    NonFinalSubclassOfSensitiveInterface
+    ObjectFinalize
+    PublicFinalizeMethod
+    SystemExit
+    UnsafeArrayDeclaration
+
+    // rulesets/serialization.xml
+    SerialPersistentFields
+    SerialVersionUID
+    SerializableClassMustDefineSerialVersionUID
+
+    // rulesets/size.xml
+    AbcComplexity   // DEPRECATED: Use the AbcMetric rule instead. Requires the GMetrics jar
+    AbcMetric   // Requires the GMetrics jar
+    ClassSize
+    CrapMetric   // Requires the GMetrics jar and a Cobertura coverage file
+    CyclomaticComplexity   // Requires the GMetrics jar
+    MethodCount
+    MethodSize
+    NestedBlockDepth
+
+    // rulesets/unnecessary.xml
+    AddEmptyString
+    ConsecutiveLiteralAppends
+    ConsecutiveStringConcatenation
+    UnnecessaryBigDecimalInstantiation
+    UnnecessaryBigIntegerInstantiation
+    UnnecessaryBooleanExpression
+    UnnecessaryBooleanInstantiation
+    UnnecessaryCallForLastElement
+    UnnecessaryCallToSubstring
+    UnnecessaryCatchBlock
+    UnnecessaryCollectCall
+    UnnecessaryCollectionCall
+    UnnecessaryConstructor
+    UnnecessaryDefInFieldDeclaration
+    //UnnecessaryDefInMethodDeclaration
+    UnnecessaryDefInVariableDeclaration
+    UnnecessaryDotClass
+    UnnecessaryDoubleInstantiation
+    UnnecessaryElseStatement
+    UnnecessaryFinalOnPrivateMethod
+    UnnecessaryFloatInstantiation
+    //UnnecessaryGString
+    //UnnecessaryGetter
+    UnnecessaryIfStatement
+    UnnecessaryInstanceOfCheck
+    UnnecessaryInstantiationToGetClass
+    UnnecessaryIntegerInstantiation
+    UnnecessaryLongInstantiation
+    UnnecessaryModOne
+    UnnecessaryNullCheck
+    UnnecessaryNullCheckBeforeInstanceOf
+    UnnecessaryObjectReferences
+    UnnecessaryOverridingMethod
+    UnnecessaryPackageReference
+    UnnecessaryParenthesesForMethodCallWithClosure
+    UnnecessaryPublicModifier
+    UnnecessaryReturnKeyword
+    UnnecessarySelfAssignment
+    UnnecessarySemicolon
+    UnnecessaryStringInstantiation
+    UnnecessarySubstring
+    UnnecessaryTernaryExpression
+    UnnecessaryTransientModifier
+
+    // rulesets/unused.xml
+    UnusedArray
+    UnusedMethodParameter
+    UnusedObject
+    UnusedPrivateField
+    UnusedPrivateMethod
+    UnusedPrivateMethodParameter
+    UnusedVariable
+
+
+}