def test_download_configs(self, outdir):
download_obj = DownloadWorkflow(pipeline="nf-core/methylseq",
revision="1.6")
download_obj.outdir = outdir
download_obj.download_configs()
assert os.path.exists(
os.path.join(outdir, "configs", "nfcore_custom.config"))
def test_download_configs(self):
outdir = tempfile.mkdtemp()
download_obj = DownloadWorkflow(pipeline="nf-core/methylseq",
release="1.6")
download_obj.outdir = outdir
download_obj.download_configs()
assert os.path.exists(
os.path.join(outdir, "configs", "nfcore_custom.config"))
def test_wf_use_local_configs(self):
# Get a workflow and configs
test_outdir = tempfile.mkdtemp()
download_obj = DownloadWorkflow(pipeline="dummy",
release="1.2.0",
outdir=test_outdir)
shutil.copytree(PATH_WORKING_EXAMPLE,
os.path.join(test_outdir, 'workflow'))
download_obj.download_configs()
# Test the function
download_obj.wf_use_local_configs()
wf_config = nf_core.utils.fetch_wf_config(
os.path.join(test_outdir, 'workflow'))
assert wf_config['params.custom_config_base'] == "'../configs/'"
def test_wf_use_local_configs(self):
# Get a workflow and configs
test_pipeline_dir = os.path.join(tempfile.mkdtemp(),
"nf-core-testpipeline")
create_obj = nf_core.create.PipelineCreate("testpipeline",
"This is a test pipeline",
"Test McTestFace",
outdir=test_pipeline_dir)
create_obj.init_pipeline()
test_outdir = tempfile.mkdtemp()
download_obj = DownloadWorkflow(pipeline="dummy",
release="1.2.0",
outdir=test_outdir)
shutil.copytree(test_pipeline_dir,
os.path.join(test_outdir, "workflow"))
download_obj.download_configs()
# Test the function
download_obj.wf_use_local_configs()
wf_config = nf_core.utils.fetch_wf_config(
os.path.join(test_outdir, "workflow"))
assert wf_config["params.custom_config_base"] == "'../configs/'"
def test_wf_use_local_configs(self, tmp_path):
# Get a workflow and configs
test_pipeline_dir = os.path.join(tmp_path, "nf-core-testpipeline")
create_obj = nf_core.create.PipelineCreate("testpipeline",
"This is a test pipeline",
"Test McTestFace",
outdir=test_pipeline_dir)
create_obj.init_pipeline()
with tempfile.TemporaryDirectory() as test_outdir:
download_obj = DownloadWorkflow(pipeline="dummy",
revision="1.2.0",
outdir=test_outdir)
shutil.copytree(test_pipeline_dir,
os.path.join(test_outdir, "workflow"))
download_obj.download_configs()
# Test the function
download_obj.wf_use_local_configs()
wf_config = nf_core.utils.fetch_wf_config(os.path.join(
test_outdir, "workflow"),
cache_config=False)
assert wf_config[
"params.custom_config_base"] == f"'{test_outdir}/workflow/../configs/'"
def test_download_configs(self):
download_obj = DownloadWorkflow(pipeline="dummy",
release="1.2.0",
outdir=tempfile.mkdtemp())
download_obj.download_configs()