search

AlexsLemonade / scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
13 stars 2 forks source link

More stub tests #334

Closed jashapiro closed 1 year ago

jashapiro commented 1 year ago

In https://github.com/AlexsLemonade/scpca-nf/pull/332, I added a stub workflow that can automatically test that workflow logic is sound without requiring a full workflow run.

Currently, the test only tests the paths used for an RNA-seq run and a CITE-seq run. We should add more test cases by adding new entries to tests/stub-metadata.tsv along with the input files to support those runs (these can generally just be blank files created with touch)

Some of the data types we should add:

We also may want to consider whether we need to test any other particular parameter flags that we set. At the moment, the only one I can think of would be --skip-genetic-demux, but we would really only be testing that it ran successfully unless we added some extra logic.

We could also add some logic to test that the expected output files/directories are generated after each run, but that gets more complicated as we add more inputs, so I'm not sold on it.

jashapiro commented 1 year ago

I think this was closed by #376