def test_param_must_have_key_and_type(saved_cwd):
Pipeline(
"test",
make_cfg("stages: [trim_bbmap]\n"
"params:\n"
" someparam:\n"
" key: A\n"
" type: int\n"
" default: 1"))
with pytest.raises(YmpConfigError):
Pipeline(
"test",
make_cfg("stages: [trim_bbmap]\n"
"params:\n"
" someparam:\n"
" type: int\n"
" default: 1"))
with pytest.raises(YmpConfigError):
Pipeline(
"test",
make_cfg("stages: [trim_bbmap]\n"
"params:\n"
" someparam:\n"
" key: A\n"
" default: 1"))
def test_pipeline_can_provide(saved_cwd):
pipe = Pipeline("test_pipe",
make_cfg("stages:\n"
" - trim_bbmap\n"
" - ref_phiX"))
assert pipe.can_provide(set(("/{sample}.R1.fq.gz", ))) == {
"/{sample}.R1.fq.gz": ".trim_bbmap"
}
def test_pipeline_path_with_param(saved_cwd):
stack = mock()
stack.name = "stack.test_pipe"
stack.stage_name = "test_pipe"
pipe = Pipeline("test_pipe",
make_cfg("stages:\n"
" - trim_bbmapQ10\n"
" - ref_phiX"))
assert pipe.get_path(stack) == "stack.trim_bbmapQ10.ref_phiX"
assert pipe.get_path(stack, "/{sample}.R1.fq.gz") == "stack.trim_bbmapQ10"
assert pipe.get_path(
stack, "/{sample}.fasta.gz") == "stack.trim_bbmapQ10.ref_phiX"
def test_parameter_must_be_mapping(saved_cwd):
with pytest.raises(YmpConfigError):
Pipeline("test",
make_cfg("stages: [trim_bbmap]\n"
"params:\n"
" someparam:"))
Pipeline(
"test",
make_cfg("stages: [trim_bbmap]\n"
"params:\n"
" someparam:\n"
" key: A\n"
" type: int\n"
" default: 1"))
def test_pipeline_stage_maybe_dict(saved_cwd):
Pipeline(
"test",
make_cfg("stages:\n"
" - trim_bbmap\n"
" - trim_bbmap:\n"
" - trim_bbmap\n"
" - trim_bbmap:\n"))
def test_stage_with_curly(saved_cwd):
pipe = Pipeline(
"test",
make_cfg("params:\n"
" tool:\n"
" key: _\n"
" type: choice\n"
" default: bbmap\n"
" value: [bbmap, sickle]\n"
"stages:\n"
" - trim_{tool}"))
assert pipe.params
def test_pipeline_must_have_stages(saved_cwd):
with pytest.raises(YmpConfigError):
Pipeline("test", make_cfg("hide: False"))
def test_params_must_be_mapping(saved_cwd):
with pytest.raises(YmpConfigError):
Pipeline("test", make_cfg("stages: [trim_bbmap]\n" "params: wrong"))
with pytest.raises(YmpConfigError):
Pipeline("test", make_cfg("stages: [trim_bbmap]\n" "params: [wrong]"))
Pipeline("test", make_cfg("stages: [trim_bbmap]\n" "params:"))
def test_stage_not_parametrizable(saved_cwd):
pipe = Pipeline("test", make_cfg("stages:\n" " - ref_phiX\n"))
assert pipe.params == []
def test_param_from_stage(saved_cwd):
pipe = Pipeline("test", make_cfg("stages: [trim_bbmap]"))
assert pipe.params
def test_pipeline_stage_name_must_not_be_empty(saved_cwd):
with pytest.raises(YmpConfigError):
Pipeline("test", make_cfg("stages:\n" " -"))