CRG-CNAG/CalliNGS-NF

Operator `phase` is deprecated

HudoGriz opened this issue · 0 comments

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