Index A | B | C | D | E | F | G | H | I | J | M | N | O | P | Q | R | S | T | U | W A Action (class in cpg_workflows.workflow) active (cpg_workflows.targets.Target attribute) add_dataset() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.MultiCohort method) add_job() (cpg_utils.dataproc.DataprocCluster method) add_other_stage_output() (cpg_workflows.workflow.StageInput method) add_sequencing_group() (cpg_workflows.targets.Dataset method) add_sequencing_group_object() (cpg_workflows.targets.Dataset method) alignment_input (cpg_workflows.targets.SequencingGroup attribute) alignment_inputs_hash (cpg_workflows.targets.Target attribute) analysis_prefix (cpg_workflows.workflow.Stage property) (cpg_workflows.workflow.Workflow property) analysis_prefix() (cpg_workflows.targets.Dataset method) append_config_paths() (in module cpg_utils.config) array() (cpg_utils.cromwell.CromwellOutputType static method) array_path() (cpg_utils.cromwell.CromwellOutputType static method) array_resource_group() (cpg_utils.cromwell.CromwellOutputType static method) as_dict() (cpg_workflows.workflow.StageInput method) (cpg_workflows.workflow.StageOutput method) as_dict_by_target() (cpg_workflows.workflow.StageInput method) as_path() (cpg_workflows.workflow.StageInput method) (cpg_workflows.workflow.StageOutput method) as_path_by_target() (cpg_workflows.workflow.StageInput method) as_path_dict_by_target() (cpg_workflows.workflow.StageInput method) as_str() (cpg_workflows.workflow.StageInput method) (cpg_workflows.workflow.StageOutput method) assays (cpg_workflows.targets.SequencingGroup attribute) authenticate_cloud_credentials_in_job() (in module cpg_utils.hail_batch) B Batch (class in cpg_utils.hail_batch) batch (cpg_utils.cromwell.CromwellBackend attribute) build_time (cpg_utils.cloud.DockerImage attribute) C CallMetadata (class in cpg_utils.cromwell_model) check_if_commit_is_on_remote() (in module cpg_utils.git) Cohort (class in cpg_workflows.targets) cohort_prefix() (cpg_workflows.workflow.Workflow method) CohortStage (class in cpg_workflows.workflow) collapse_status_of_calls() (in module cpg_utils.cromwell_model) color() (cpg_utils.cromwell_model.ExecutionStatus method) command() (in module cpg_utils.hail_batch) config_retrieve() (in module cpg_utils.config) ConfigError copy_common_env() (in module cpg_utils.hail_batch) cpg_namespace() (in module cpg_utils.hail_batch) cpg_test_dataset_path() (in module cpg_utils.config) (in module cpg_utils.hail_batch) cpg_utils module cpg_utils.cloud module cpg_utils.config module cpg_utils.cromwell module cpg_utils.cromwell_model module cpg_utils.dataproc module cpg_utils.git module cpg_utils.hail_batch module cpg_workflows.targets module cpg_workflows.workflow module cram (cpg_workflows.targets.SequencingGroup attribute) cram_stage_name (cpg_workflows.targets.SequencingGroup attribute) create() (cpg_workflows.targets.Dataset static method) create_cohort() (cpg_workflows.targets.MultiCohort method) create_dataset() (cpg_workflows.targets.Cohort method) CromwellBackend (class in cpg_utils.cromwell) CromwellOutputType (class in cpg_utils.cromwell) D dad (cpg_workflows.targets.PedigreeInfo attribute) dataproc_requires_public_ip_address_flag() (in module cpg_utils.dataproc) DataprocCluster (class in cpg_utils.dataproc) Dataset (class in cpg_workflows.targets) dataset_path() (in module cpg_utils.config) DatasetStage (class in cpg_workflows.workflow) DefaultOverrideServiceBackend (class in cpg_utils.hail_batch) deprecated_queue_for_cohort() (cpg_workflows.workflow.CohortStage method) (cpg_workflows.workflow.DatasetStage method) (cpg_workflows.workflow.SequencingGroupStage method) (cpg_workflows.workflow.Stage method) display() (cpg_utils.cromwell_model.CallMetadata method) (cpg_utils.cromwell_model.WorkflowMetadataModel method) DockerImage (class in cpg_utils.cloud) done (cpg_utils.cromwell_model.ExecutionStatus attribute) E email_from_id_token() (in module cpg_utils.cloud) ExecutionStatus (class in cpg_utils.cromwell_model) expected_outputs() (cpg_workflows.workflow.CohortStage method) (cpg_workflows.workflow.DatasetStage method) (cpg_workflows.workflow.MultiCohortStage method) (cpg_workflows.workflow.SequencingGroupStage method) (cpg_workflows.workflow.Stage method) external_id (cpg_workflows.targets.SequencingGroup property) F failed (cpg_utils.cromwell_model.ExecutionStatus attribute) fam_id (cpg_workflows.targets.PedigreeInfo attribute) fasta_res_group() (in module cpg_utils.hail_batch) FEMALE (cpg_workflows.targets.Sex attribute) find_image() (in module cpg_utils.cloud) forced (cpg_workflows.targets.Target attribute) G genome_build() (in module cpg_utils.config) get_access_level() (in module cpg_utils.config) get_alignment_inputs_hash() (cpg_workflows.targets.Target method) get_batch() (in module cpg_utils.hail_batch) get_cohort_by_id() (cpg_workflows.targets.MultiCohort method) get_cohorts() (cpg_workflows.targets.MultiCohort method) get_config() (in module cpg_utils.config) get_config_paths() (in module cpg_utils.config) get_cpg_namespace() (in module cpg_utils.config) get_cromwell_oauth_token() (in module cpg_utils.cromwell) get_dataproc_driver_image_from_hail_version() (in module cpg_utils.dataproc) get_dataset_by_name() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.MultiCohort method) get_datasets() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.MultiCohort method) get_driver_image() (in module cpg_utils.config) get_gcloud_set_project() (in module cpg_utils.config) get_gcp_project() (in module cpg_utils.config) get_git_branch_name() (in module cpg_utils.git) get_git_commit_ref_of_current_repository() (in module cpg_utils.git) get_git_default_remote() (in module cpg_utils.git) get_git_repo_root() (in module cpg_utils.git) get_google_identity_token() (in module cpg_utils.cloud) get_init_script_from_hail_version() (in module cpg_utils.dataproc) get_job_attrs() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.Dataset method) (cpg_workflows.targets.MultiCohort method) (cpg_workflows.targets.SequencingGroup method) (cpg_workflows.targets.Target method) (cpg_workflows.workflow.Stage method) get_job_prefix() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.Dataset method) (cpg_workflows.targets.SequencingGroup method) (cpg_workflows.targets.Target method) get_jobs() (cpg_workflows.workflow.StageInput method) get_organisation_name_from_current_directory() (in module cpg_utils.git) get_organisation_name_from_remote() (in module cpg_utils.git) get_output_of_command() (in module cpg_utils.git) get_path_components_from_gcp_path() (in module cpg_utils.cloud) get_ped_dict() (cpg_workflows.targets.PedigreeInfo method) (cpg_workflows.targets.SequencingGroup method) get_project_id_from_service_account_email() (in module cpg_utils.cloud) get_readable_duration() (in module cpg_utils.cromwell_model) get_relative_path_from_git_root() (in module cpg_utils.git) get_relative_script_path_from_git_root() (in module cpg_utils.git) get_repo_name_from_current_directory() (in module cpg_utils.git) get_repo_name_from_remote() (in module cpg_utils.git) get_script_directory_from_hail_version() (in module cpg_utils.dataproc) get_seconds_duration_between_cromwell_dates() (in module cpg_utils.cromwell_model) get_sequencing_group_ids() (cpg_workflows.targets.Target method) get_sequencing_groups() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.Dataset method) (cpg_workflows.targets.MultiCohort method) (cpg_workflows.targets.SequencingGroup method) (cpg_workflows.targets.Target method) get_stage_cohort_prefix() (cpg_workflows.workflow.Stage method) get_wheel_from_hail_version() (in module cpg_utils.dataproc) get_workflow() (in module cpg_workflows.workflow) guess_script_github_url_from() (in module cpg_utils.git) guess_script_name_from_script_argument() (in module cpg_utils.git) gvcf (cpg_workflows.targets.SequencingGroup attribute) gvcf_stage_name (cpg_workflows.targets.SequencingGroup attribute) H hail_dataproc_job() (in module cpg_utils.dataproc) hash_from_list_of_strings() (in module cpg_workflows.targets) I image_path() (in module cpg_utils.config) (in module cpg_utils.hail_batch) in_progress (cpg_utils.cromwell_model.ExecutionStatus attribute) init_batch() (in module cpg_utils.hail_batch) is_finished() (cpg_utils.cromwell_model.ExecutionStatus method) is_member_in_cached_group() (in module cpg_utils.cloud) J jar_spec (cpg_utils.hail_batch.DefaultOverrideServiceBackend property) jobs (cpg_workflows.workflow.StageOutput attribute) M make_cram_path() (cpg_workflows.targets.SequencingGroup method) make_gvcf_path() (cpg_workflows.targets.SequencingGroup method) make_job_name() (in module cpg_utils.hail_batch) make_outputs() (cpg_workflows.workflow.Stage method) make_sv_evidence_path (cpg_workflows.targets.SequencingGroup property) MALE (cpg_workflows.targets.Sex attribute) meta (cpg_workflows.targets.SequencingGroup attribute) (cpg_workflows.workflow.StageOutput attribute) module cpg_utils cpg_utils.cloud cpg_utils.config cpg_utils.cromwell cpg_utils.cromwell_model cpg_utils.dataproc cpg_utils.git cpg_utils.hail_batch cpg_workflows.targets cpg_workflows.workflow mom (cpg_workflows.targets.PedigreeInfo attribute) MultiCohort (class in cpg_workflows.targets) MultiCohortStage (class in cpg_workflows.workflow) N name (cpg_utils.cloud.DockerImage attribute) (cpg_workflows.workflow.Stage property) O output_by_target (cpg_workflows.workflow.Stage attribute) output_path() (in module cpg_utils.config) (in module cpg_utils.hail_batch) output_version (cpg_workflows.workflow.Workflow property) P parse() (cpg_utils.cromwell_model.CallMetadata static method) (cpg_utils.cromwell_model.WorkflowMetadataModel static method) (cpg_workflows.targets.Sex static method) participant_id (cpg_workflows.targets.SequencingGroup property) path_walk() (in module cpg_workflows.workflow) pedigree (cpg_workflows.targets.SequencingGroup attribute) PedigreeInfo (class in cpg_workflows.targets) phenotype (cpg_workflows.targets.PedigreeInfo attribute) pipelines_api (cpg_utils.cromwell.CromwellBackend attribute) prefix (cpg_workflows.workflow.Stage property) (cpg_workflows.workflow.Workflow property) prefix() (cpg_workflows.targets.Dataset method) prepare_git_job() (in module cpg_utils.hail_batch) prepare_inner_calls_string() (in module cpg_utils.cromwell_model) preparing (cpg_utils.cromwell_model.ExecutionStatus attribute) prepend_config_paths() (in module cpg_utils.config) Q query_command() (in module cpg_utils.hail_batch) QUEUE (cpg_workflows.workflow.Action attribute) queue_for_multicohort() (cpg_workflows.workflow.CohortStage method) (cpg_workflows.workflow.DatasetStage method) (cpg_workflows.workflow.MultiCohortStage method) (cpg_workflows.workflow.SequencingGroupStage method) (cpg_workflows.workflow.Stage method) queue_jobs() (cpg_workflows.workflow.CohortStage method) (cpg_workflows.workflow.DatasetStage method) (cpg_workflows.workflow.MultiCohortStage method) (cpg_workflows.workflow.SequencingGroupStage method) (cpg_workflows.workflow.Stage method) queued_stages (cpg_workflows.workflow.Workflow attribute) queuedincromwell (cpg_utils.cromwell_model.ExecutionStatus attribute) R read_configs() (in module cpg_utils.config) read_secret() (in module cpg_utils.cloud) reference_path() (in module cpg_utils.config) (in module cpg_utils.hail_batch) remote_tmpdir() (in module cpg_utils.hail_batch) required_stages (cpg_workflows.workflow.Stage attribute) required_stages_classes (cpg_workflows.workflow.Stage attribute) reset_batch() (in module cpg_utils.hail_batch) retryablefailure (cpg_utils.cromwell_model.ExecutionStatus attribute) REUSE (cpg_workflows.workflow.Action attribute) rich_id (cpg_workflows.targets.SequencingGroup property) rich_id_map() (cpg_workflows.targets.Target method) run() (cpg_utils.hail_batch.Batch method) (cpg_workflows.workflow.Workflow method) run_batch_job_and_print_url() (in module cpg_utils.hail_batch) run_cromwell_workflow() (in module cpg_utils.cromwell) run_cromwell_workflow_from_repo_and_get_outputs() (in module cpg_utils.cromwell) run_timestamp (cpg_workflows.workflow.Workflow attribute) run_workflow() (in module cpg_workflows.workflow) running (cpg_utils.cromwell_model.ExecutionStatus attribute) S sequencing_group (cpg_workflows.targets.PedigreeInfo attribute) SequencingGroup (class in cpg_workflows.targets) SequencingGroupStage (class in cpg_workflows.workflow) set_alignment_inputs_hash() (cpg_workflows.targets.Target method) set_config_paths() (in module cpg_utils.config) set_stages() (cpg_workflows.workflow.Workflow method) setup_dataproc() (in module cpg_utils.dataproc) Sex (class in cpg_workflows.targets) sex (cpg_workflows.targets.PedigreeInfo attribute) single() (cpg_utils.cromwell.CromwellOutputType static method) single_path() (cpg_utils.cromwell.CromwellOutputType static method) single_resource_group() (cpg_utils.cromwell.CromwellOutputType static method) size (cpg_utils.cloud.DockerImage attribute) SKIP (cpg_workflows.workflow.Action attribute) skip() (in module cpg_workflows.workflow) Stage (class in cpg_workflows.workflow) stage() (in module cpg_workflows.workflow) StageInput (class in cpg_workflows.workflow) StageInputNotFoundError StageOutput (class in cpg_workflows.workflow) start_query_context() (in module cpg_utils.hail_batch) starting (cpg_utils.cromwell_model.ExecutionStatus attribute) succeeded (cpg_utils.cromwell_model.ExecutionStatus attribute) symbol() (cpg_utils.cromwell_model.ExecutionStatus method) T tag_uri (cpg_utils.cloud.DockerImage attribute) Target (class in cpg_workflows.targets) target_id (cpg_workflows.targets.Cohort property) (cpg_workflows.targets.Dataset property) (cpg_workflows.targets.MultiCohort property) (cpg_workflows.targets.SequencingGroup property) (cpg_workflows.targets.Target property) tmp_prefix (cpg_workflows.workflow.Stage property) (cpg_workflows.workflow.Workflow property) tmp_prefix() (cpg_workflows.targets.Dataset method) to_tsv() (cpg_workflows.targets.Cohort method) try_get_ar_guid() (in module cpg_utils.config) U UNKNOWN (cpg_workflows.targets.Sex attribute) UnsuppliedDefault (class in cpg_utils.config) unwrap_caused_by() (in module cpg_utils.cromwell_model) update_dict() (in module cpg_utils.config) uri (cpg_utils.cloud.DockerImage attribute) W watch_workflow() (in module cpg_utils.cromwell) watch_workflow_and_get_output() (in module cpg_utils.cromwell) web_prefix (cpg_workflows.workflow.Stage property) (cpg_workflows.workflow.Workflow property) web_prefix() (cpg_workflows.targets.Dataset method) web_url() (cpg_workflows.targets.Dataset method) (in module cpg_utils.config) (in module cpg_utils.hail_batch) Workflow (class in cpg_workflows.workflow) WorkflowError WorkflowMetadataModel (class in cpg_utils.cromwell_model) write_ped_file() (cpg_workflows.targets.Cohort method) (cpg_workflows.targets.Dataset method) (cpg_workflows.targets.MultiCohort method) write_secret() (in module cpg_utils.cloud)