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

[rarthur-eicc]

Description of the bug

Hi,

After upgrading to 2.5, I am noticing an error with failed samples that do not meet the 1000 read mapped threshold. We use this for negative controls and thus expect to see these fail, but it usually generates a little summary email with the number of aligned reads per failed sample. This isn't happening, and this is the part of the .nextflow.log I think is relevant to this:

Jul-15 08:53:47.620 [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: 54: Unexpected character: '\'' @ line 54, column 53.
   fail_mapped_reads.sort().join('</code></
                                 ^

1 error

	at groovy.text.GStringTemplateEngine$GStringTemplate.<init>(GStringTemplateEngine.java:200)
	at groovy.text.GStringTemplateEngine.createTemplate(GStringTemplateEngine.java:114)
	at groovy.text.TemplateEngine.createTemplate(TemplateEngine.java:58)
	at groovy.text.TemplateEngine$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$4.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
	at Script_cbf077bf$_runScript_closure3.doCall(Script_cbf077bf:652)
	at Script_cbf077bf$_runScript_closure3.doCall(Script_cbf077bf)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
	at groovy.lang.Closure.call(Closure.java:412)
	at groovy.lang.Closure.call(Closure.java:406)
	at nextflow.script.WorkflowMetadata$_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:675)
	at nextflow.Session.destroy(Session.groovy:625)
	at nextflow.script.ScriptRunner.terminate(ScriptRunner.groovy:222)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:122)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:337)
	at nextflow.cli.Launcher.run(Launcher.groovy:480)
	at nextflow.cli.Launcher.main(Launcher.groovy:639)

I've attached the nextflow.log and my samplesheet used to parse this. It won't let me upload a .sh file, so I've changed it to .txt and included it here.

Command used and terminal output

The command to invoke viralrecon 2.5 was:
`nextflow run nf-core/viralrecon -profile docker --input samplesheet.csv --platform illumina --protocol amplicon --genome 'MN908947.3' --primer_bed swift_refv3_primers.bed --ivar_trim_offset 5 --skip_assembly --skip_kraken2 --multiqc_config '/home/rarthur/new_multiqc_config.yaml' --email 'rarthu3@emory.edu' --outdir ./results`

Relevant files

nextflow.log
samplesheet.csv
water_only.txt

System information

No response

[NeginValizadegan]

The problem still persists. Any plans to fix this in viralrecon pipeline?

[drpatelh]

This should be fixed now in dec2a21 so closing this issue @rarthur-eicc @NeginValizadegan . It was an issue with the HTML syntax used for the email code.

Be great if you can test the dev version of the pipeline before we release. Feel free to re-open if the problem persists.

nextflow pull nf-core/viralrecon -r dev
nextflow run nf-core/viralrecon -r dev <YOUR_PARAMETERS>

[NeginValizadegan]

This should be fixed now in dec2a21 so closing this issue @rarthur-eicc @NeginValizadegan . It was an issue with the HTML syntax used for the email code.

Be great if you can test the dev version of the pipeline before we release. Feel free to re-open if the problem persists.

nextflow pull nf-core/viralrecon -r dev
nextflow run nf-core/viralrecon -r dev <YOUR_PARAMETERS>

Thanks! I will check it out and let you know. Thanks!

[NeginValizadegan]

This should be fixed now in dec2a21 so closing this issue @rarthur-eicc @NeginValizadegan . It was an issue with the HTML syntax used for the email code.

Be great if you can test the dev version of the pipeline before we release. Feel free to re-open if the problem persists.

nextflow pull nf-core/viralrecon -r dev
nextflow run nf-core/viralrecon -r dev <YOUR_PARAMETERS>

I checked this with the dev branch and it's working now :) Thanks for fixing it and sorry for the delay. I wanted to try it out on the new project we'll receive hence the delay. When are you expecting to update the master branch?

[drpatelh]

No worries! The pipeline was released last week. You can now run with -r 2.6.0

[NeginValizadegan]

No worries! The pipeline was released last week. You can now run with -r 2.6.0

ha ha I tried 2.6 and it didn't work. I missed the 0 at the end. Thanks!