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import os
import pytest
from utils import assert_files_equal, datapath, cutpath
from cutadapt.cli import main
from cutadapt.report import Statistics
@pytest.fixture(params=[1, 2])
def cores(request):
return request.param
@pytest.fixture
def run(tmp_path):
def _run(params, expected, inpath) -> Statistics:
if type(params) is str:
params = params.split()
params += ["--json", os.fspath(tmp_path / "stats.cutadapt.json")]
tmp_fastaq = tmp_path / expected
params += ["-o", tmp_fastaq]
params += [datapath(inpath)]
stats = main([str(p) for p in params])
# TODO redirect standard output
assert_files_equal(cutpath(expected), tmp_fastaq)
return stats
return _run
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