pepkit/example_peps

Some simple examples of PEP-compatible projects

Install

pip install --user --upgrade https://github.com/pepkit/pepkit/archive/master.zip

Install dev version

pip install --user --upgrade https://github.com/pepkit/pepkit/archive/dev.zip

example_peps's Issues

Add prefix to data file path

I have a project where input filenames cannot be derived from sample attributes, but are determined by the outside provider. I would still like to use PEP to simplify my sample list.

Is there a way to simply add a prefix to the path for a data file?
For example, I would like to have project-id/external_id_L001.fastq.gz in my sample configuration, and then extend this into /current/path/for/data/files/project-id/external_id_L001.fastq.gz. This seems like a simple enough use case, is this possible using PEP?

Examples for new features

@stolarczyk Do you have any example PEPs for the new PEP 2.1.0 features, like no config file?

pipeline interface example

add an example with a pipeline interface (multiple ones) that can be then used in pepr and BiocProject vignettes, docs examples and unit tests

related to pepkit/BiocProject#36

Include pipeline_interface.yaml files?

Since these example peps are linked from looper (https://github.com/pepkit/looper), would it be a good idea to include pipeline_interface.yaml files with each example, so that looper can be run?