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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
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conpair channel bug #1014

Closed anoronh4 closed 3 weeks ago

anoronh4 commented 4 months ago

I receive this error:

Jul-19 01:58:52.631 [Actor Thread 79] ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: Script_67fa09d92ea6cc0d$_runScript_closure3$_closure5$_closure21.call() is applicable for argument types: (ArrayList) values: [[s_mel6_PDX1, s_C_LUL6W6_N002_d02, [/juno/cmo/ccs/noronhaa/pdx_project/workspace/work/3b/365ecce35e50cdceaa5d2314a578a2/s_mel6_PDX1__s_C_LUL6W6_N002_d02.concordance.txt, ...]]]
Possible solutions: any(), any(), any(groovy.lang.Closure), tap(groovy.lang.Closure), each(groovy.lang.Closure), any(groovy.lang.Closure)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:266)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:814)
        at groovy.lang.GroovyObject.invokeMethod(GroovyObject.java:39)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:44)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
        at jdk.internal.reflect.GeneratedMethodAccessor199.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        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:1030)
        at groovy.lang.Closure.call(Closure.java:427)
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
        at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
        at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
        at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
        at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
        at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
        at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)
Jul-19 01:58:53.060 [Actor Thread 79] DEBUG nextflow.Session - Session aborted -- Cause: No signature of method: Script_67fa09d92ea6cc0d$_runScript_closure3$_closure5$_closure21.call() is applicable for argument types: (ArrayList) values: [[s_mel6_PDX1, s_C_LUL6W6_N002_d02, [/juno/cmo/ccs/noronhaa/pdx_project/workspace/work/3b/365ecce35e50cdceaa5d2314a578a2/s_mel6_PDX1__s_C_LUL6W6_N002_d02.concordance.txt, ...]]]
Possible solutions: any(), any(), any(groovy.lang.Closure), tap(groovy.lang.Closure), each(groovy.lang.Closure), any(groovy.lang.Closure)

Looks like the channel has 3 elements: [idTumor, idNormal, conpairFiles] But the downstream operator is expecting 4: [placeHolder, idTumor, idNormal, conpairFiles]