Pipeable commands

Introduction

Since the release of Biopet v0.5.0 we support piping of programs/tools to decrease disk usage and run time. Here we make use of fifo piping, which enables a developer to very easily implement piping for most pipeable tools.

Example

    val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) ::
      Some(gsnapCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten)
    pipe.threadsCorrection = -1
    zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
    zcatR2.foreach(_._1.foreach(x => pipe.threadsCorrection -= 1))
    add(pipe)
    ar._2

• In the above example we define the variable pipe. This is the place to define which jobs should be piped together. In this case we perform a zcat on the input files. After that GSNAP alignment and Picard reordersam is performed. The final output of this job will be a SAM file. All intermediate files will be removed as soon as the job finished completely without any error codes.
• With the second command pipe.threadsCorrection = -1 we make sure the total number of assigned cores is not too high. This ensures that the job can still be scheduled to the compute cluster.
• So we hope you can appreciate in the above example that we decrease the total number of assigned cores with 2. This is done by the command zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)