biowdl / compare-gff

A pipeline to compare a General Feature Format file to other General Feature Format files.

Pipeline-template

A multisample wdl-template.

The structure:

• A pipeline that executes jobs over all samples and starts the scatters per:
  • Sample. executes jobs per sample and starts the scatters per:
    • library. Executes jobs per library and starts the scaters per:
      • readgroup. Executes jobs per readgroup.

Then there is sampleConfig.wdl. This determines hoe samples libraries and readgroups are related by a samples.yml file.