Testing environment for fireflow.

The main purpose (so far) is to verify that fireflow has support for opening a large variety of files conveniently (that is, by only using configuration flags to repair non-compliance).

Note that data integrity (that is, ensuring that the data in the file is the same data that is actually presented) is at least partly covered by the unit tests in fireflow itself.

See the config for a list of all files currently being tested. Under test_files, the next layer of keys correspond to Flow Repository (FR) IDs, and the layer of keys under this correspond to file names in each FR dataset. Each FR dataset must be obtained manually and unzipped into resources/fcs/<FR_ID> with the listed FCS files in the root of this directory.

Ensure you have mamba (or conda for the patient) installed.

Clone this repo and navigate to the root. Run the following:

mamba env create -f env.yml

Then run the pipeline:

snakemake -c 20 --use-conda --configfile=config/config.yml all

Any files that "fail" parsing will produce a failed snakemake job. This means that they would not be fully standardized given the data they contain and the provided options.

A list of all tested machines with their serial numbers and software can be seen at results/reports/machines.tsv.

Files which have been standardized can be viewed at results/read_test/fcs. Each of these should be identical to the original except that every non-compliant issue has been fixed.

Flow Repository is currently quite finicky and not permitting downloads. Will likely switch to ImmPort after figuring out their API.