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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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Operator `phase` is deprecated #35

Open HudoGriz opened 1 year ago

HudoGriz commented 1 year ago

When trying to run nextflow run CRG-CNAG/CalliNGS-NF -profile docker with the N E X T F L O W ~ version 22.10.3 I receive the following error: Operator 'phase' is deprecated -- it will be removed in a future release.

Checking the log reveals:

Dec-06 14:15:45.034 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.DeprecationException: Operator `phase` is deprecated -- it will be removed in a future release
    at nextflow.extension.OpCall.checkDeprecation(OpCall.groovy:327)
    at nextflow.extension.OpCall.invoke1(OpCall.groovy:319)
    at nextflow.extension.OpCall.invoke0(OpCall.groovy:306)
    at nextflow.extension.OpCall.invoke(OpCall.groovy:166)
    at nextflow.extension.OpCall.call(OpCall.groovy:113)
    at nextflow.plugin.extension.PluginExtensionProvider.invokeExtensionMethod(PluginExtensionProvider.groovy:279)
    at groovy.runtime.metaclass.NextflowDelegatingMetaClass.invokeMethod(NextflowDelegatingMetaClass.java:59)
    at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:44)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
    at Script_6487ce9d.group_per_sample(Script_6487ce9d:371)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at nextflow.script.FunctionDef.invoke_a(FunctionDef.groovy:65)
    at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:41)
    at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:94)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
    at Script_3558d273$_runScript_closure1$_closure2.doCall(Script_3558d273:122)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
    at groovy.lang.Closure.call(Closure.java:412)
    at groovy.lang.Closure.call(Closure.java:406)
    at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205)
    at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189)
    at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
    at nextflow.script.ChainableDef$invoke_a.call(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
    at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:208)
    at nextflow.script.BaseScript.run(BaseScript.groovy:217)
    at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:230)
    at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:225)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:131)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:354)
    at nextflow.cli.Launcher.run(Launcher.groovy:487)
    at nextflow.cli.Launcher.main(Launcher.groovy:646)

I would appreciate any advice that helps me get forward.

Much obliged,

Blaž