Pipeline fails at email step: Failed to invoke workflow.onComplete event handler

[RoganGrant]

Description of the bug

On version 3.8.1, I have run into an issue where the pipeline runs entirely without issue through the final multiqc step, but fails at the final email output with the error: Failed to invoke 'workflow.onComplete' event handler. Per @drpatelh this may not actually be nf-core specific, as it has been reported recently with viralrecon as well: Issue 320. Based on the .nextflow.log (see attached), it seems it may just be some sort of syntax issue with the nf-core template.

From .nextflow.log:

Jul-27 22:27:37.427 [main] ERROR nextflow.script.WorkflowMetadata - Failed to invoke workflow.onComplete event handler
groovy.lang.GroovyRuntimeException: Failed to parse template script (your template may contain an error or be trying to use expressions not currently supported): startup failed:
GStringTemplateScript2.groovy: 45: Unexpected character: ''' @ line 45, column 48.
de>${fail_percent_mapped.join('</
^

1 error

at groovy.text.GStringTemplateEngine$GStringTemplate.(GStringTemplateEngine.java:200)
at groovy.text.GStringTemplateEngine.createTemplate(GStringTemplateEngine.java:114)
at groovy.text.TemplateEngine.createTemplate(TemplateEngine.java:58)
at groovy.text.TemplateEngine$createTemplate.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 NfcoreTemplate.email(NfcoreTemplate.groovy:113)
at NfcoreTemplate$email$4.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at Script_010ba6cd$_runScript_closure3.doCall(Script_010ba6cd:815)
at Script_010ba6cd$_runScript_closure3.doCall(Script_010ba6cd)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:406)
at nextflow.script.WorkflowMetadata$_invokeOnComplete_closure4.doCall(WorkflowMetadata.groovy:389)
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:274)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at groovy.lang.Closure.call(Closure.java:412)
at groovy.lang.Closure.call(Closure.java:428)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2358)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2343)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2384)
at nextflow.script.WorkflowMetadata.invokeOnComplete(WorkflowMetadata.groovy:387)
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 groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1268)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1029)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1012)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:101)
at nextflow.script.WorkflowMetadata$_closure3.doCall(WorkflowMetadata.groovy:252)
at nextflow.script.WorkflowMetadata$_closure3.call(WorkflowMetadata.groovy)
at nextflow.Session.shutdown0(Session.groovy:671)
at nextflow.Session.destroy(Session.groovy:621)
at nextflow.script.ScriptRunner.terminate(ScriptRunner.groovy:222)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:122)
at nextflow.cli.CmdRun.run(CmdRun.groovy:308)
at nextflow.cli.Launcher.run(Launcher.groovy:480)
at nextflow.cli.Launcher.main(Launcher.groovy:639)

Command used and terminal output

nextflow run nf-core/rnaseq \
-r '3.8.1' \
-profile nu_genomics \
--email [email] \
--additional_fasta '/home/rag0151/[dir]/transgenes.fa' \
--star_index false \
--genome 'GRCm38' \
-work-dir [dir] \
--input ~/[dir]/220727_nfcore_samplesheet.csv \
--outdir [dir]

Relevant files

nextflow.log

System information

Nextflow version: 21.10.5.5658
Hardware: HPC
Executor: slurm
Container engine: Singularity
OS: Red Hat Enterprise Linux Server release 7.5 (Maipo)
Version of nf-core/rnaseq: 3.8.1

[drpatelh]

Fixed in #875