Main script class name collides with variable names in global scope

[manuelesimi]

The onComplete event handler seems to fail when nextflow is running on an ubuntu machine.
The error reported is:

ERROR ~ No signature of method: static workflow.onComplete() is applicable for argument types: (workflow$_run_closure2) values: [workflow$_run_closure2@25e2ab5a]

Here's a simple workflow that I used to the error:

#!/usr/bin/env nextflow
_stringToEcho = ['Hello from $HOSTNAME'].channel()
process EchoStringToStandardOut {

input:
val stringToEcho from _stringToEcho

output:
stdout echo into _echo

shell:

    '''
echo  "!{stringToEcho}"
    '''
}
workflow.onComplete {
println "Workflow execution summary"
println "---------------------------"
println "Workflow completed at: $workflow.complete"
println "Duration: ${workflow.duration}"
println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
if (!  workflow.success) {
println "Error message: $workflow.errorMessage"
}
println "Files generated by the execution are available in $workflow.workDir"
println "---------------------------"

The same workflow executed on a Mac works well.
This is the configuration of the two machines as reported in the .nextflow.log:

Mac OS machine runtime:

  Version: 0.17.3 build 3495
  Modified: 18-02-2016 11:00 UTC (06:00 EDT)
  System: Mac OS X 10.10.2
  Runtime: Groovy 2.4.5 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_51-b16

Ubuntu manchine runtime:

  Version: 0.17.3 build 3495
  Modified: 18-02-2016 11:00 UTC
  System: Linux 3.13.0-74-generic
  Runtime: Groovy 2.4.5 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_72-b15
  Encoding: UTF-8 (UTF-8)

Attached is the full log reported by nextflow when running on ubuntu and failing.

nextflow.txt

[pditommaso]

Hi Manuele,

What if you run this command:

echo "workflow.onComplete { println 'DONE' }" | nextflow run - 

[manuelesimi]

That works:

ubuntu@frontend001:~$ echo "workflow.onComplete { println 'DONE' }" | nextflow run - 
N E X T F L O W  ~  version 0.17.3
DONE
ubuntu@frontend001:~$

[pditommaso]

I'm unable to replicate problem. What if you remove the process part in the script you have posted?

[manuelesimi]

Now it's very minimal but I still get the error:

ubuntu@frontend001:~$ cat workflow.nf

workflow.onComplete {
println "---------------------------"
}

ubuntu@frontend001:~$ nextflow workflow.nf

N E X T F L O W  ~  version 0.17.3
Launching workflow.nf
ERROR ~ No signature of method: static workflow.onComplete() is applicable for argument types: (workflow$_run_closure1) values: [workflow$_run_closure1@1359c03a]

-- Check script 'workflow.nf' at line: 1 or see '.nextflow.log' file for more details
ubuntu@frontend001:~$

[pditommaso]

I'm starting to think there's a hidden special character in your script, otherwise it should fail also the one liner

[manuelesimi]

You might be right. But I'm unable to detect it.
I wrote from scratch another workflow script (named workflow2.nf) on the ubuntu machine, exactly the same than the one that I scp-ed from mac to ubuntu:

ubuntu@frontend001:~$ cat workflow.nf 
workflow.onComplete { println 'DONE' }
ubuntu@frontend001:~$ cat workflow2.nf 
workflow.onComplete { println 'DONE' }

If I look at their bytes, it's confirmed that they are exactly the same:

ubuntu@frontend001:~$ od -c workflow.nf 
0000000   w   o   r   k   f   l   o   w   .   o   n   C   o   m   p   l
0000020   e   t   e       {       p   r   i   n   t   l   n       '   D
0000040   O   N   E   '       }  \n
0000047
ubuntu@frontend001:~$ od -c workflow2.nf 
0000000   w   o   r   k   f   l   o   w   .   o   n   C   o   m   p   l
0000020   e   t   e       {       p   r   i   n   t   l   n       '   D
0000040   O   N   E   '       }  \n
0000047

But then, when I execute them, the results are completely different:

ubuntu@frontend001:~$ nextflow workflow.nf 
N E X T F L O W  ~  version 0.17.3
Launching workflow.nf
ERROR ~ No signature of method: static workflow.onComplete() is applicable for argument types: (workflow$_run_closure1) values: [workflow$_run_closure1@a93621]

 -- Check script 'workflow.nf' at line: 1 or see '.nextflow.log' file for more details

ubuntu@frontend001:~$ nextflow workflow2.nf 
N E X T F L O W  ~  version 0.17.3
Launching workflow2.nf
DONE

[pditommaso]

Oh, I got it. You named that script workflow also before, isn't right? Nextflow scripts are compiled to a Java class having the same name as the file, thus in your case the class name overrides the implicit workflow variable raising that exception (!)

[manuelesimi]

bingo!
You are right. I renamed the file and it works!
I guess you should have a runtime check in nextflow that validates the filename, if that's a constraint. And that should happen for all the implicit objects used inside a workflow script.
In the NextflowWorkbench we will add such checks too, so the user is informed as soon as it types the workflow name.

[pditommaso]

I think I can manage to generate a class name with a random suffix that will prevent this problem.

[manuelesimi]

That should fix for good the issue.