Add integration test for post processing of flat flow cell demultiplexed with bclconvert

[seallard]

Description

This PR adds an integration test for the post processing of a flow cell demultiplexed with bclconvert using the flat output directory structure. Part of project https://github.com/Clinical-Genomics/project-planning/issues/482.

Fixed

• Add integration test for post processing of flat flow cell demultiplexed with bclconvert

This version is a

• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[Vince-janv]

Nice! If you want to avoid duplicating code I think you could make use of the parametrize functionality in pytest, to run the same test with separate inputs.

[seallard]

Nice! If you want to avoid duplicating code I think you could make use of the parametrize functionality in pytest, to run the same test with separate inputs.

I tried to find a way to parametrise a test with fixtures, but it is not supported yet by pytest directly as far as I understand pytest-dev/pytest#349

[Vince-janv]

Nice! If you want to avoid duplicating code I think you could make use of the parametrize functionality in pytest, to run the same test with separate inputs.

I tried to find a way to parametrise a test with fixtures, but it is not supported yet by pytest directly as far as I understand pytest-dev/pytest#349

Right, we've encountered this before. What has been done before is creating a third fixture, aggregating them and then using the keys to parametrize. Feel free to implement it if you like it. Otherwise don't 😊

@pytest.fixture(name="flowcell_directories", scope="session")
fixture_flowcell_directories(flow_cell_directory_name_demultiplexed_with_bcl_convert_flat,flow_cell_directory_name_demultiplexed_with_bcl_convert_not_flat) -> dict:
    return {"FLAT":flow_cell_directory_name_demultiplexed_with_bcl_convert_flat,"TREE":flow_cell_directory_name_demultiplexed_with_bcl_convert_not_flat}

@pytest.mark.parametrize(
    "order_type",
    ["FLAT", "TREE"],
)
def test_whatever(
    structure: str,
    flowcell_directories: dict
    some_function(flowcell_directories[structure])

[ChrOertlin]

Looks good, make it much easier and cleans up the fixtures. Just the sample_internal_id variables. I think I caught them all with my suggested commits.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

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