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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: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
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
The text was updated successfully, but these errors were encountered:
Sorry for the late reply, probably not useful for you anymore but just someone finds this issue in the future.
The problem is that this parameter expects an integer as you can see in the docs, here
Description of the bug
Tried to run the pipeline with the
--trim_nextseq
. However, Nextflow throws an error after barely a couple of seconds: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
System information
Nextflow v23.10.0.5889
Ran on Canadian HPC
Slurm
Singularity
Pipeline v2.0.0
The text was updated successfully, but these errors were encountered: