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nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.
https://nf-co.re/chipseq
MIT License
177 stars 144 forks source link

Error with NextSeq trimming #375

Open gitMakeCoffee opened 6 months ago

gitMakeCoffee commented 6 months ago

Description of the bug

Tried to run the pipeline with the --trim_nextseq. However, Nextflow throws an error after barely a couple of seconds:

N E X T F L O W  ~  version 23.10.0
ERROR ~ Unable to parse config file: '/lustre/project/123456/user/.NEXTFLOW/nf-core-chipseq_2.0.0/2_0_0/nextflow.config'

  Cannot compare java.lang.Boolean with value 'true' and java.lang.Integer with value '0'

 -- Check '.nextflow.log' file for details

Strangely, this error resolves once the option is removed, and the pipeline launches correctly.

Command used and terminal output

nextflow run -profile singularity,cluster -c $HOME/.nextflow/moreTime.config -with-report report.html -with-dag dag.png -with-timeline timeline.html --genome GRCh38 --input sampleSheet.csv --read_length 50 --outdir result

Relevant files

Dec.-21 21:13:00.392 [main] DEBUG nextflow.cli.Launcher - $> nextflow run -profile singularity,cluster -c $HOME/.nextflow/moreTime.config -with-report report.html -with-dag dag.png -with-timeline timeline.html --genome GRCh38 --input sampleSheet.csv --read_length 50 --outdir result
Dec.-21 21:13:00.455 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.10.0
Dec.-21 21:13:00.476 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/user/.nextflow/plugins; core-plugins: nf-amazon@2.1.4,nf-azure@1.3.2,nf-cloudcache@0.3.0,nf-codecommit@0.1.5,nf-console@1.0.6,nf-ga4gh@1.1.0,nf-google@1.8.3,nf-tower@1.6.3,nf-wave@1.0.0
Dec.-21 21:13:00.487 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Dec.-21 21:13:00.488 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Dec.-21 21:13:00.491 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Dec.-21 21:13:00.500 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Dec.-21 21:13:01.375 [main] DEBUG nextflow.config.ConfigBuilder - Found config home: /home/user/.nextflow/config
Dec.-21 21:13:01.375 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /lustre/project/123456/user/.NEXTFLOW/nf-core-chipseq_2.0.0/2_0_0/nextflow.config
Dec.-21 21:13:01.377 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/user/.nextflow/moreTime.config
Dec.-21 21:13:01.378 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/user/.nextflow/config
Dec.-21 21:13:01.378 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /lustre/project/123456/user/.NEXTFLOW/nf-core-chipseq_2.0.0/2_0_0/nextflow.config
Dec.-21 21:13:01.378 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/user/.nextflow/moreTime.config
Dec.-21 21:13:01.386 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity,cluster`
Dec.-21 21:13:01.442 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity,cluster`
Dec.-21 21:13:02.917 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/lustre/project/123456/user/.NEXTFLOW/nf-core-chipseq_2.0.0/2_0_0/nextflow.config'

  Cannot compare java.lang.Boolean with value 'true' and java.lang.Integer with value '0'

java.lang.IllegalArgumentException: Cannot compare java.lang.Boolean with value 'true' and java.lang.Integer with value '0'
    at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.compareToWithEqualityCheck(DefaultTypeTransformation.java:598)
    at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.compareTo(DefaultTypeTransformation.java:533)
    at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.compareTo(ScriptBytecodeAdapter.java:716)
    at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.compareGreaterThan(ScriptBytecodeAdapter.java:766)
    at Script7B611291D57182C185BC9F045AD67BCA$_run_closure4$_closure58.doCall(Script7B611291D57182C185BC9F045AD67BCA:148)
    at Script7B611291D57182C185BC9F045AD67BCA$_run_closure4$_closure58.doCall(Script7B611291D57182C185BC9F045AD67BCA)
    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:1030)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
    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:130)
    at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:427)
    at jdk.internal.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
    at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
    at groovy.lang.MetaObjectProtocol$invokeMethod$0.call(Unknown Source)
    at nextflow.config.ConfigBase$_includeConfig_closure2.doCall(ConfigBase.groovy:114)
    at jdk.internal.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
    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 org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
    at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
    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 groovy.lang.Script.invokeMethod(Script.java:96)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:348)
    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:185)
    at Script7B611291D57182C185BC9F045AD67BCA$_run_closure4.doCall(Script7B611291D57182C185BC9F045AD67BCA:145)
    at Script7B611291D57182C185BC9F045AD67BCA$_run_closure4.doCall(Script7B611291D57182C185BC9F045AD67BCA)
    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:1030)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
    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:130)
    at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:427)
    at jdk.internal.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
    at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
    at groovy.lang.MetaObjectProtocol$invokeMethod$0.call(Unknown Source)
    at nextflow.config.ConfigBase$_includeConfig_closure2.doCall(ConfigBase.groovy:114)
    at jdk.internal.reflect.GeneratedMethodAccessor12.invoke(Unknown Source)
    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 org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
    at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
    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:185)
    at Script7B611291D57182C185BC9F045AD67BCA.run(Script7B611291D57182C185BC9F045AD67BCA:144)
    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 groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
    at groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1042)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1128)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
    at groovy.lang.Closure.call(Closure.java:427)
    at groovy.lang.Closure.call(Closure.java:406)
    at java_util_concurrent_Callable$call.call(Unknown Source)
    at nextflow.config.ConfigBase.includeConfig(ConfigBase.groovy:115)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.reflection.CachedMethod$invoke.call(Unknown Source)
    at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:448)
    at jdk.internal.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
    at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:226)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
    at _nf_config_444ac8c6.run(_nf_config_444ac8c6:239)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.reflection.CachedMethod$invoke.call(Unknown Source)
    at nextflow.config.ConfigParser$_parse_closure5.doCall(ConfigParser.groovy:448)
    at jdk.internal.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaMethod.invoke(ClosureMetaMethod.java:83)
    at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1118)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
    at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
    at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:130)
    at nextflow.config.ConfigParser.parse(ConfigParser.groovy:476)
    at nextflow.config.ConfigParser$parse$0.callCurrent(Unknown Source)
    at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
    at nextflow.config.ConfigParser$parse$0.callCurrent(Unknown Source)
    at nextflow.config.ConfigParser.parse(ConfigParser.groovy:303)
    at nextflow.config.ConfigParser$parse$6.call(Unknown Source)
    at nextflow.config.ConfigBuilder.parse0(ConfigBuilder.groovy:434)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
    at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:420)
    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.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
    at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:203)
    at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:370)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
    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:194)
    at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:315)
    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.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:48)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:189)
    at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:57)
    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:185)
    at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:806)
    at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:819)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:324)
    at nextflow.cli.Launcher.run(Launcher.groovy:499)
    at nextflow.cli.Launcher.main(Launcher.groovy:670)
Caused by: java.lang.ClassCastException: class java.lang.Integer cannot be cast to class java.lang.Boolean (java.lang.Integer and java.lang.Boolean are in module java.base of loader 'bootstrap')
    at java.base/java.lang.Boolean.compareTo(Boolean.java:45)
    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 groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1254)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
    at org.codehaus.groovy.runtime.InvokerHelper.invokePojoMethod(InvokerHelper.java:1024)
    at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1015)
    at org.codehaus.groovy.runtime.typehandling.DefaultTypeTransformation.compareToWithEqualityCheck(DefaultTypeTransformation.java:584)
    ... 185 common frames omitted

System information

Nextflow v23.10.0.5889 Ran on Canadian HPC Slurm Singularity Pipeline v2.0.0