FeaturesΒΆ

Simplicity for the beginning, power when you need to expand.

  • Flexible pipelines:
    Use looper with any pipeline, any library, in any domain. We designed it to work with pypiper, but looper has an infinitely flexible command-line argument system that will let you configure it to work with any script (pipeline) that accepts command-line arguments. You can also configure looper to submit multiple pipelines per sample.
  • Flexible compute:
    If you don’t change any settings, looper will simply run your jobs serially. But Looper includes a templating system that will let you process your pipelines on any cluster resource manager (SLURM, SGE, etc.). We include default templates for SLURM and SGE, but it’s easy to add your own as well. Looper also gives you a way to determine which compute queue/partition to submit on-the-fly, by passing the --compute parameter to your call to looper run, making it simple to use by default, but very flexible if you have complex resource needs.
  • Standardized project definition:
    Looper reads a flexible standard format for describing projects, which we call PEP (Portable Encapsulated Projects). Once you describe your project in this format, other PEP-compatible tools can also read your project. For example, you may use the pepr R package or the (pending) pep python package to import all your sample metadata (and pipeline results) in an R or python analysis environment. With a standardized project definition, the possibilities are endless.
  • Subprojects:
    Subprojects make it easy to define two very similar projects without duplicating project metadata.
  • Job completion monitoring:
    Looper is job-aware and will not submit new jobs for samples that are already running or finished, making it easy to add new samples to existing projects, or re-run failed samples.
  • Flexible input files:
    Looper’s derived column feature makes projects portable. You can use it to collate samples with input files on different file systems or from different projects, with different naming conventions. How it works: you specify a variable filepath like /path/to/{sample_name}.txt, and looper populates these file paths on the fly using metadata from your sample sheet. This makes it easy to share projects across compute environments or individuals without having to change sample annotations to point at different places.
  • Flexible resources:
    Looper has an easy-to-use resource requesting scheme. With a few lines to define CPU, memory, clock time, or anything else, pipeline authors can specify different computational resources depending on the size of the input sample and pipeline to run. Or, just use a default if you don’t want to mess with setup.