The PEP filters are an experimental feature and may change in feature versions of eido

Eido filters

Eido provides a CLI to convert a PEP into different output formats. These include some built-in formats, like csv (which takes your spits out a processed csv file, with project/sample modified), yaml, and a few others. It also provides a plugin system so that you can write your own Python functions to provide custom output formats.

View available filters

Run this command to see what filters are available:

eido filters

You'll see some output like this. There are a few built-in filters available:

Available filters:
 - basic
 - csv
 - yaml
 - yaml-samples

You can also write a custom filters, which will write your PEP into whatever format you need.

Convert a PEP into an alternative format with a filter

To convert a PEP into an output format, do this:

eido convert config.yaml -f basic
running plugin pep
Project 'pepconvert' (/home/nsheff/code/pepconvert/config.yaml)
5 samples: WT_REP1, WT_REP2, RAP1_UNINDUCED_REP1, RAP1_UNINDUCED_REP2, RAP1_IAA_30M_REP1
Sections: pep_version, sample_table, subsample_table
...

This basic format just lists the config file, the number of samples and their names, and identifies the sections in the project config file. Another format is -f yaml,

eido convert config.yaml -f yaml

This will output your samples in yaml format.

Parametrizing PEP conversions

The filter functions are parameterizable, so depending on the desired filter function design and required arguments you might need to provide them like this:

eido convert config.yaml -f yaml -a argument1=value1 argument2=value2