Cannot get property 'args' on null object error

[creamerk]

Hi, Thanks for building this pipeline! I'm running into an error that I haven't been able to solve, copied below. Thanks in advance!

command: nextflow run nf-core/bactmap -profile test,singularity

error seen:

Cannot get property 'args' on null object
 -- Check script '/home/kcreamer/.nextflow/assets/nf-core/bactmap/./workflows/bactmap.nf' at line: 38 or see '.nextflow.log' file for more details

Line 38 in the script I believe is: multiqc_options.args += params.multiqc_title ? Utils.joinModuleArgs(["--title \"$params.multiqc_title\""]) : ''

(I thus tried running the same command but with multiqc turned off, ie nextflow run nf-core/bactmap -profile test,singularity --skip_multiqc but the same null args error occurred).

And the info in the .nextflow.log reads:

May-10 13:29:18.605 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot get property 'args' on null object
May-10 13:29:18.637 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NullPointerException: Cannot get property 'args' on null object
        at org.codehaus.groovy.runtime.NullObject.getProperty(NullObject.java:60)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:194)
        at org.codehaus.groovy.runtime.callsite.NullCallSite.getProperty(NullCallSite.java:46)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGetProperty(AbstractCallSite.java:329)
        at Script_c99ee09b.runScript(Script_c99ee09b:38)
        at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
        at nextflow.script.BaseScript.run(BaseScript.groovy:203)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:206)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:200)
        at nextflow.script.IncludeDef.memoizedMethodPriv$loadModule0PathMapSession(IncludeDef.groovy:142)
        at nextflow.script.IncludeDef.access$0(IncludeDef.groovy)
        at nextflow.script.IncludeDef$__clinit__closure1.doCall(IncludeDef.groovy)
        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 org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
        at nextflow.script.IncludeDef.loadModule0(IncludeDef.groovy)
        at nextflow.script.IncludeDef.load0(IncludeDef.groovy:114)
        at nextflow.script.IncludeDef$load0$1.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 Script_14934cd2.runScript(Script_14934cd2:28)
        at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
        at nextflow.script.BaseScript.run(BaseScript.groovy:203)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:220)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:334)
        at nextflow.cli.Launcher.run(Launcher.groovy:480)
        at nextflow.cli.Launcher.main(Launcher.groovy:639

I tried running another nf-core pipeline (nf-core/mag) and it got past this step & didn't return the same "null args" error, so it seems so far to be specific to this pipeline.

Specs:

• Nextflow Version: 22.04.0
• SingularityPRO version 3.5-8.el7
• System: Linux 3.10.0-1160.45.1.el7.x86_64
• Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.9.1-internal+0-adhoc..src
• nf-core/bactmap v1.0.0
• Nextflow was called from an activated conda environment; singularity was also pre-loaded.

Thanks in advance for your help with this!

[andersgs]

The issue is that test.conf doesn't have config details for multiqc, and other tools. At the moment, it only has config info for bcftools_filter and alignpseudogenomes.

[craigwindell]

We have noticed that with Nextflow 21.04.1, the pipeline test profile completes successfully.

Later versions such as 22.04.04 fail with the Cannot get property 'args' on null object message