varlociraptor custom scenario parameter issue

[ahwanpandey]

Hello,

I am using SAREK v3.9.0.

When I use the following in my params file, everything works fine:

"varlociraptor_scenario_somatic": null

As soon as I point it to an actual file (for example pointing to the same file as it would have pulled if the parameter was null), I get an error even before SAREK submits any jobs.

"varlociraptor_scenario_somatic": "/researchers/user/Tools/omics_tools/nf-core/nf-core-sarek/3_9_0/assets/varlociraptor_somatic.yte.yaml"

This is the error:

July-10 15:51:50.855 [Actor Thread 5] ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingMethodException: No signature of method: Script_bd2e4c9d2a46d63c$_runScript_closure1$_closure2$_closure4.call() is applicable for argument types: (LinkedList) values: [[[id:66130_PrimaryFFPE_v
s_66130_GL, normal_id:66130_GL, patient:S66130, sex:XX, ...], ...]]
Possible solutions: any(), any(), any(groovy.lang.Closure), each(groovy.lang.Closure), tap(groovy.lang.Closure), any(groovy.lang.Closure)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:272)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:790)
        at groovy.lang.GroovyObject.invokeMethod(GroovyObject.java:39)
        at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151)
        at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
        at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
        at jdk.internal.reflect.GeneratedMethodAccessor127.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:343)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
        at groovy.lang.Closure.call(Closure.java:433)
        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:840)

I also updated the "yaml" file to the actual contamination and sex values, rather than $contamination and $sex_string. So I dont think thats the problem?

I am not 100% sure but maybe it is the parsing of the varlociraptor parameter that is the issue here?

sarek/main.nf

Line 326 in b97952e

params.varlociraptor_scenario_somatic ? channel.fromPath(params.varlociraptor_scenario_somatic).map { it -> [[id: it.baseName - '.yte'], it] }.collect() : channel.fromPath("${projectDir}/assets/varlociraptor_somatic.yte.yaml").collect(),

Please help!

Thanks,
Ahwan

[ahwanpandey]

Hello, any help with this please? Thanks!

[ahwanpandey]

Hi @FriederikeHanssen would you be able to have a look at this issue. Would really appreciate it! Thanks!