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