isEmpty error on empty msisensorpro file channel for GRCh38 #24
Description
Description of the bug
Nice work on this pipeline everyone. Looks great.
I was testing this on some of our genomes and received a recurrent error when running or aligning GrCh38 genomes. It looks like the msisensor reference data for these don't exist, in which case they are run dynamically.
In subworkflows/local/prepare_genome/main.nf...
if (msisensorpro_list.isEmpty()) { MSISENSORPRO_SCAN(fasta) msisensorpro_list = MSISENSORPRO_SCAN.out.list.map{ meta, list -> list } // path: genome_msi.list }
... is used to check if the msisensorpro_list file channel is empty. Apparently (at least in nf 23.04.0) isEmpty can't be used on file channels.
I was able to bypass this by changing this to...
if (!params.msisensorpro_list) {
Hope this helps.
Error
Jun-17 16:31:27.955 [main] DEBUG nextflow.Session - Session aborted -- Cause: Missing process or function isEmpty()
Jun-17 16:31:28.002 [main] DEBUG nextflow.Session - The following nodes are still active:
[operator] map
[operator] map
[operator] tap
[operator] groupTuple
[operator] map
[operator] combine
[operator] map
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] map
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
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[operator] collect
[operator] collect
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[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] map
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] collect
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] branch
[operator] map
[operator] map
[operator] filter
[operator] branch
[operator] map
[operator] map
[operator] filter
[operator] branch
[operator] map
[operator] map
[operator] filter
[operator] branch
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
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[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
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[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
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[operator] map
[operator] map
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[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
[operator] filter
[operator] map
[operator] map
Jun-17 16:31:28.233 [main] ERROR nextflow.cli.Launcher - @unknown
nextflow.exception.MissingProcessException: Missing process or function isEmpty()
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:191)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
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:176)
at Script_6120566a$_runScript_closure119$_closure136.doCall(Script_6120566a:908)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
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:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
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:176)
at Script_c6ff89b0$_runScript_closure1$_closure3.doCall(Script_c6ff89b0:146)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
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:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
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:176)
at Script_c6ff89b0$_runScript_closure2$_closure4.doCall(Script_c6ff89b0:160)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
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:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
at nextflow.script.ChainableDef$invoke_a.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
at nextflow.script.BaseScript.run0(BaseScript.groovy:183)
at nextflow.script.BaseScript.run(BaseScript.groovy:192)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:229)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:224)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:130)
at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
at nextflow.cli.Launcher.run(Launcher.groovy:494)
at nextflow.cli.Launcher.main(Launcher.groovy:653)
Caused by: groovy.lang.MissingMethodException: No signature of method: groovyx.gpars.dataflow.DataflowQueue.isEmpty() is applicable for argument types: () values: []
Possible solutions: identity(groovy.lang.Closure), isBound(), dump(), inspect(), dump()
at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:70)
at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:46)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
at Script_7c6867ce$_runScript_closure1$_closure2.doCall(Script_7c6867ce:50)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
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:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
... 79 common frames omitted
Command used and terminal output
Relevant files
No response
System information
No response