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We essentially just run salmontools on this test data and then compare the output file against an existing output file asserting their checksums match.
Below are the tests in their current implementation.
Context
Currently we fetch test data for salmontools from an external repo.
refinebio/workers/run_tests.sh
Line 82 in c4b4a6a
We essentially just run salmontools on this test data and then compare the output file against an existing output file asserting their checksums match.
Below are the tests in their current implementation.
double read
https://github.com/AlexsLemonade/refinebio/blob/dev/workers/data_refinery_workers/processors/test_salmon.py#L572
single read
https://github.com/AlexsLemonade/refinebio/blob/dev/workers/data_refinery_workers/processors/test_salmon.py#L612
Problem or idea
Since the data is no longer available we need to recreate this data. I believe we are considering using Polyester rna-seq to generate this.
Solution or next step
Tagging @jaclyn-taroni @jashapiro for next steps.
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