Input prefix inaccurate at first pipeline stage

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Create file 'test.groovy' with this content:
count_lines = {
   if (SKIP == 1) {
      exec """
         echo "Not counting lines"
      """
      forward input
   } else {
      transform("count") {
         exec """
            echo "Counting lines" &&
            wc -l $input > $output
         """
      }
   }
}

report = {
   println("Input prefix is: " + input.prefix)
}

Bpipe.run {
   count_lines + report
}

2. Run: bpipe run -p SKIP=0 -d out_dir/ test.groovy primers.fna
Notice screen output: "Input prefix is: out_dir//primers"

3. Now run: bpipe run -p SKIP=1 -d out_dir/ test.groovy primers.fna
Notice screen output: "Input prefix is: primers"

What is the expected output? What do you see instead?
In both cases, it is expected that the input prefix would be "out_dir//primers"

What version of the product are you using? On what operating system?
Bpipe 0.9.8.5
Linux x86_64

Original issue reported on code.google.com by florent....@gmail.com on 17 Mar 2014 at 6:48