pallassgj / bpipe

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java.lang.NullPointerException when mixing "%" and .using(..) #94

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
What steps will reproduce the problem?

test.bpipe file:

s = {
   exec "echo $bla"
}

run {
   "%"*[s.using(bla:"-w"), s.using(bla:"-B")]
}

command line:
 bpipe run test1.bpipe file_1.bam file_2.bam

What is the expected output? What do you see instead?
Expected:
-B 
-B 
-w 
-w

Actual:
================================================================================
====================
|                              Starting Pipeline at 2014-03-18 20:45            
                   |
================================================================================
====================

======================================= Stage s [file_1.bam] 
=======================================

======================================= Stage s [file_2.bam] 
=======================================

======================================= Stage s [file_2.bam] 
=======================================

======================================= Stage s [file_1.bam] 
=======================================
java.lang.NullPointerException
        at bpipe.PipelineDelegate.propertyMissing(PipelineDelegate.groovy:159)
        at bpipe.PipelineDelegate.getProperty(PipelineDelegate.groovy)
        at script13952007065911381402844$_run_closure1.doCall(script13952007065911381402844.groovy:2)
        at bpipe.ParameterizedClosure.call(ParameterizedClosure.groovy:67)
        at bpipe.ParameterizedClosure.doCall(ParameterizedClosure.groovy:71)
        at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
        at bpipe.PipelineStage$_runBody_closure4.doCall(PipelineStage.groovy:282)
        at bpipe.PipelineStage$_runBody_closure4.doCall(PipelineStage.groovy)
        at bpipe.PipelineStage.runBody(PipelineStage.groovy:281)
        at bpipe.PipelineStage.this$2$runBody(PipelineStage.groovy)
        at bpipe.PipelineStage.run(PipelineStage.groovy:211)
        at bpipe.Pipeline.runSegment(Pipeline.groovy:476)
        at bpipe.Pipeline$runSegment$1.call(Unknown Source)
        at bpipe.PipelineCategory$_splitOnMap_closure9_closure32.doCall(PipelineCategory.groovy:422)
        at bpipe.PipelineCategory$_splitOnMap_closure9_closure32.doCall(PipelineCategory.groovy)
-w
-w
-B
Pipeline failed! (2)

One or more parallel stages aborted. The following messages were reported:

null

======================================== Pipeline Finished 
=========================================

What version of the product are you using? On what operating system?

bpipe-0.9.8.6_beta_3 
on linux 

Please provide any additional information below.

Passing in one file instead of 2 avoids the error:
 bpipe run test1.bpipe file_1.bam

Original issue reported on code.google.com by ben.weisburd on 19 Mar 2014 at 3:47