[BUG] Cannot invoke method containsKey() on null object

I'm trying vsn-pipelines following your vignette here: https://vsn-pipelines-examples.readthedocs.io/en/latest/index.html

But when I'm running config, error comes;

In log file; Apr-08 18:14:38.832 [main] DEBUG nextflow.cli.Launcher - $> nextflow -c com.config run vib-singlecell-nf/vsn-pipelines -entry scenic -r v0.25.0 Apr-08 18:14:39.057 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.3 Apr-08 18:14:42.062 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/.git/config; branch: master; remote: origin; url: https://github.com/vib-singlecell-nf/vsn-pipelines.git Apr-08 18:14:42.107 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/.git/config; branch: master; remote: origin; url: https://github.com/vib-singlecell-nf/vsn-pipelines.git Apr-08 18:14:43.330 [main] INFO nextflow.cli.CmdRun - Launching vib-singlecell-nf/vsn-pipelines [hopeful_bassi] - revision: 721c42f889 [v0.25.0] Apr-08 18:14:44.234 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/nextflow.config Apr-08 18:14:44.244 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/users/hcjangimmuno/com.config Apr-08 18:14:44.245 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/nextflow.config Apr-08 18:14:44.245 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/users/hcjangimmuno/com.config Apr-08 18:14:44.266 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Apr-08 18:14:45.447 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: standard Apr-08 18:14:45.975 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/home/users/hcjangimmuno/.nextflow/plugins Apr-08 18:14:46.007 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Apr-08 18:14:46.019 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins local root: .nextflow/plr/empty Apr-08 18:14:46.041 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-08 18:14:46.043 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-08 18:14:46.056 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-08 18:14:46.101 [main] INFO org.pf4j.AbstractPluginManager - No plugins Apr-08 18:14:46.228 [main] DEBUG nextflow.Session - Session uuid: b72845a8-d20e-4657-84c4-e7c38509d0da Apr-08 18:14:46.228 [main] DEBUG nextflow.Session - Run name: hopeful_bassi Apr-08 18:14:46.255 [main] DEBUG nextflow.Session - Executor pool size: 24 Apr-08 18:14:46.322 [main] DEBUG nextflow.cli.CmdRun - Version: 21.04.3 build 5560 Created: 21-07-2021 15:09 UTC (22-07-2021 00:09 KDT) System: Linux 3.10.0-862.el7.x86_64 Runtime: Groovy 3.0.7 on OpenJDK 64-Bit Server VM 1.8.0_292-b10 Encoding: UTF-8 (ANSI_X3.4-1968) Process: 192293@bnode15 [10.0.2.15] CPUs: 24 - Mem: 1007.8 GB (66.5 GB) - Swap: 0 (0) Apr-08 18:14:46.406 [main] DEBUG nextflow.Session - Work-dir: /home/users/hcjangimmuno/work [lustre] Apr-08 18:14:46.407 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/users/hcjangimmuno/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/bin Apr-08 18:14:46.431 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Apr-08 18:14:46.461 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Apr-08 18:14:47.736 [main] DEBUG nextflow.Session - Session start invoked Apr-08 18:14:47.741 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/users/hcjangimmuno/out/nextflow_reports/execution_trace.txt Apr-08 18:14:49.572 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Apr-08 18:14:53.640 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: COMPRESS_HDF5, SCFILE_CONVERTER_FROM_SCE, SC__FILE_CONCATENATOR, SCPUBLISH, SC__STAR_CONCATENATOR, SC__FILE_CONVERTER Apr-08 18:14:53.990 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot invoke method containsKey() on null object Apr-08 18:14:54.021 [main] DEBUG nextflow.Session - The following nodes are still active: [operator] view

Apr-08 18:14:54.043 [main] ERROR nextflow.cli.Launcher - @unknown java.lang.NullPointerException: Cannot invoke method containsKey() on null object at org.codehaus.groovy.runtime.NullObject.invokeMethod(NullObject.java:91) 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.NullCallSite.call(NullCallSite.java:34) 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_7c29aa5e.runScript(Script_7c29aa5e:9) at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170) at nextflow.script.BaseScript.run(BaseScript.groovy:200) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:221) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:207) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:201) at nextflow.script.IncludeDef.memoizedMethodPriv$loadModule0PathMapSession(IncludeDef.groovy:142) at nextflow.script.IncludeDef.access$0(IncludeDef.groovy) at nextflow.script.IncludeDef$clinitclosure1.doCall(IncludeDef.groovy) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) 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:263) 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$2.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at Script_fc2ccf76$_runScript_closure21$_closure75.doCall(Script_fc2ccf76:735) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovy.lang.Closure.call(Closure.java:406) at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:186) at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:170) at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52) at nextflow.script.ChainableDef$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:191) at nextflow.script.BaseScript.run(BaseScript.groovy:200) at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:221) at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:212) at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:120) at nextflow.cli.CmdRun.run(CmdRun.groovy:302) at nextflow.cli.Launcher.run(Launcher.groovy:475) at nextflow.cli.Launcher.main(Launcher.groovy:657)

How can I solve this problem? my nextflow version 21.04.3, and pipelines is [v0.25.0]

vib-singlecell-nf / vsn-pipelines

[BUG] Cannot invoke method containsKey() on null object #378