How to create automatic sample groups

The imply modifier lets you set global, group-level attributes at the project level instead of duplicating that information for every sample that belongs to a group of samples. This makes your project more portable and does a better job conceptually with separating sample attributes from project attributes.

Example

sample_modifiers:
  imply:
    - if:
        genome: ["hg18", "hg19", "hg38"]
      then:
        organism: "human"
    - if:
        genome: ["mm9", "mm10"]
      then:
        organism: "mouse"  
    - if:
        organism: ["human", "mouse", "Mouse"]
      then:
        family: "mammal"
    - if:
        organism: ["bird", "jay", "cardinal"]
      then:
        family: "aves"

In this example we expect the samples will have existing genome attributes. The first and second implications will set an organism attribute to either human or mouse, depending on the value in the genome attribute. The next implication then adds a new variable, family, with the value mammal for any samples with human or mouse as the organism.

We've therefore used implied attributes to automatically create sample groups on the basis of existing attributes. We could then use the value in family, for example, to do a differential comparison on these samples. Any new samples added to the table in the original format will immediately work with any downstream tools.