def test_cwl_rnaseq(self, install_test_files):
with install_cwl_test_files() as work_dir:
with utils.chdir(os.path.join(work_dir, "rnaseq")):
if os.path.exists("cromwell_work"):
shutil.rmtree("cromwell_work")
subprocess.check_call(
["bcbio_vm.py", "cwlrun", "cromwell", "rnaseq-workflow"])
def test_cwl_local_somatic_workflow(self, install_test_files):
with install_cwl_test_files() as workdir:
with utils.chdir(os.path.join(workdir, "somatic")):
subprocess.check_call(["bash", "./run_generate_cwl.sh"])
if os.path.exists("cwltool_work"):
shutil.rmtree("cwltool_work")
subprocess.check_call(["bash", "./run_cwltool.sh"])
def test_cwl_docker_joint_calling_workflow(self):
with install_cwl_test_files() as workdir:
with utils.chdir(os.path.join(workdir, "gvcf_joint")):
subprocess.check_call(["bash", "./run_generate_cwl.sh"])
if os.path.exists("cromwell_work"):
shutil.rmtree("cromwell_work")
subprocess.check_call(["bash", "./run_cromwell.sh"])
def test_cwl_arvados_workflow(self, install_test_files):
"""Requires ARVADOS_API_HOST and ARVADOS_API_TOKEN set"""
if os.environ.get("ARVADOS_API_HOST") and os.environ.get(
"ARVADOS_API_TOKEN"):
with install_cwl_test_files() as workdir:
with utils.chdir(os.path.join(workdir, "arvados")):
subprocess.check_call(["bash", "./run_generate_cwl.sh"])
def test_cwl_docker_somatic_workflow(self):
with install_cwl_test_files() as workdir:
with utils.chdir(os.path.join(workdir, "somatic")):
subprocess.check_call(["bash", "./run_generate_cwl.sh"])
if os.path.exists("cromwell_work"):
shutil.rmtree("cromwell_work")
subprocess.check_call(["bcbio_vm.py", "cwlrun", "cromwell", "somatic-workflow"])
def test_4_cwl_rnaseq(self, install_test_files, data_dir):
"""CWL: run a RNA-seq workflow using Docker.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "rnaseq")):
cl = ["bash", "./run_generate_cwl.sh"]
if os.path.exists("toil_work"):
shutil.rmtree("toil_work")
cl = ["bash", "./run_toil.sh"]
subprocess.check_call(cl)
def test_4_cwl_rnaseq(self, install_test_files, data_dir):
"""CWL: run a RNA-seq workflow using Docker.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "rnaseq")):
cl = ["bash", "./run_generate_cwl.sh"]
if os.path.exists("cromwell_work"):
shutil.rmtree("cromwell_work")
cl = ["bcbio_vm.py", "cwlrun", "cromwell", "rnaseq-workflow"]
subprocess.check_call(cl)
def test_5_cwl_arvados(self, install_test_files, data_dir):
"""CWL: prepare workflow for running on Arvados.
Requires ARVADOS_API_HOST and ARVADOS_API_TOKEN set
"""
if os.environ.get("ARVADOS_API_HOST") and os.environ.get("ARVADOS_API_TOKEN"):
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "arvados")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
def test_3_cwl_docker_joint(self, data_dir):
"""CWL: run a gVCF based joint-calling workflow using Docker.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "gvcf_joint")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
if os.path.exists("bunny_work"):
shutil.rmtree("bunny_work")
cl = ["bash", "./run_bunny.sh"]
subprocess.check_call(cl)
def test_2_cwl_docker_somatic(self, data_dir):
"""CWL: run a somatic workflow using Docker.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "somatic")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
if os.path.exists("toil_work"):
shutil.rmtree("toil_work")
cl = ["bash", "./run_toil.sh"]
subprocess.check_call(cl)
def test_5_cwl_arvados(self, install_test_files, data_dir):
"""CWL: prepare workflow for running on Arvados.
Requires ARVADOS_API_HOST and ARVADOS_API_TOKEN set
"""
if os.environ.get("ARVADOS_API_HOST") and os.environ.get(
"ARVADOS_API_TOKEN"):
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "arvados")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
def test_1_cwl_local(self, install_test_files, data_dir):
"""CWL: prepare somatic workflow and run on local installation.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "somatic")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
if os.path.exists("cwltool_work"):
shutil.rmtree("cwltool_work")
cl = ["bash", "./run_cwltool.sh"]
subprocess.check_call(cl)
def test_1_cwl_local(self, install_test_files, data_dir):
"""CWL: prepare somatic workflow and run on local installation.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "somatic")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
if os.path.exists("cwltool_work"):
shutil.rmtree("cwltool_work")
cl = ["bash", "./run_cwltool.sh"]
subprocess.check_call(cl)
def test_3_cwl_docker_joint(self, data_dir):
"""CWL: run a gVCF based joint-calling workflow using Docker.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "gvcf_joint")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
if os.path.exists("bunny_work"):
shutil.rmtree("bunny_work")
cl = ["bash", "./run_bunny.sh"]
subprocess.check_call(cl)
def test_2_cwl_docker_somatic(self, data_dir):
"""CWL: run a somatic workflow using Docker.
"""
with install_cwl_test_files(data_dir) as workdir:
with utils.chdir(os.path.join(workdir, "somatic")):
cl = ["bash", "./run_generate_cwl.sh"]
subprocess.check_call(cl)
if os.path.exists("cwltoil_work"):
shutil.rmtree("cwltoil_work")
cl = ["bash", "./run_toil.sh"]
subprocess.check_call(cl)
