pytest_ngsfixtures.wm package¶
Submodules¶
pytest_ngsfixtures.wm.snakemake module¶
-
pytest_ngsfixtures.wm.snakemake.
run
(snakefile, target='all', save=False, **kwargs)[source]¶ Run snakemake on snakefile.
Wraps snakefile in a command string and pass the string to shell wrapper.
Examples
from pytest_ngsfixtures.wm import snakemake for r in snakemake.run("/path/to/Snakefile", target="test.bam", options=["--ri -k"], iterable=True): print(r)
Parameters: - snakefile (str, py._path.local.LocalPath) – snakefile full path name
- target (str) – snakemake target to run
- options (list) – options to pass to snakemake
- save (bool) – save shell script with command
- Kwargs:
- See
pytest_ngsfixtures.shell.shell
documentation.
Returns: Results from shell
.
-
pytest_ngsfixtures.wm.snakemake.
snakefile
(request, tmpdir_factory)[source]¶ Return a temporary directory path object pointing to the location of a Snakefile.
If no snakefile is defined with pytest.mark.snakefile, the fixture will assume there is a Snakefile in the same directory as the calling test file.
Examples
@pytest.mark.snakefile(snakefile="/path/to/Snakefile", dirname="foo") def test_snakefile(snakefile): print(snakefile.listdir())