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pallassgj / bpipe

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Transform should not overwrite input files if output file would be produced with same name as input #54

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
It's possible to construct a transform() that will make an output file the same 
name as an input file and destroy the input. eg:

transform("bam") {
  exec "command $input.bed $input.bam > $output"
}

Bpipe should notice that the output file is going to have the same name as an 
input (or output from previous stage) and prevent that happening.

Original issue reported on code.google.com by ssade...@gmail.com on 14 Aug 2012 at 3:26