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)