How to mix and match amendments on the fly

At times you will want to create two projects that are very similar, but differ just in one or two attributes. For example, you may define a project with one set of samples, and then want an identical project but using a different sample annotation sheet. Or, you may define a project to run on a particular reference genome, and want to define a second project that is identical, but uses a different reference genome.

You could simply define 2 complete PEPs, but this would duplicate information and make it harder to maintain. Instead, you can use amendments, which allow you to encode additional similar projects all within the original project_config.yaml file. Amendments are like mini embedded project_config.yaml files that can be activated by software. When a PEP is parsed, you may specify one or more included amendments, which will amend the values in the processed PEP. This is a powerful function that can be used for many purposes, such as on the fly tweaks or embedding multiple subprojects within a parent project.

Example

sample_table: annotation.csv
genome: hg38
project_modifiers:
  amend:
    my_project2:
      sample_table: annotation2.csv
    my_project3:
      sample_table: annotation3.csv
    hg19_analysis:
      genome: hg19
...

If you load this configuration file, it will by default use the annotation.csv file, and the genome attribute will be set to "hg38". There are 3 amendments available: my_project2, my_project3,a nd hg19_analysis. If you activate my_project2, by passing amendments=my_project2 when parsing the PEP, the resulting object will use the annotation2.csv sample_table instead of the default annotation.csv -- still run on "hg38". To run two amendments, you could issue ammendments=my_project2,hg19_analysis, which will result in this config file:

sample_table: annotation2.csv
genome: hg19
project_modifiers:
  amend:
    ...

Practically what happens under the scenes is that the primary project is first loaded, and then, if an amendment is activated, it overrides any attributes with those specified in the amendment.

How do you activate an amendment?

Activating an amendment depends on what software you're using to load your PEP. A PEP-compliant implementation must define some way to activate amendments. For example, you can activate amendments in peppy or pepr by passing an argument, amendments=my_project2, when you construct the Project object.

Can you activate multiple amendments?

Yes! Amendments are passed and parsed as a priority list; so the first amendment is processed, and then the next one, and so on. So, the final amendment in the list has the highest priority.