Index

A

AbstractCmd (class in snakemake.parser) AbstractExecutor (class in snakemake.executors) AbstractJob (class in snakemake.jobs) AbstractRemoteObject (class in snakemake.remote) AbstractRemoteProvider (class in snakemake.remote) accession (snakemake.remote.NCBI.RemoteObject property) add() (snakemake.report.RuleRecord method) (snakemake.rules.Ruleorder method) add_command() (snakemake.executors.TibannaExecutor method) add_rule() (snakemake.workflow.Workflow method) add_workflow_files() (snakemake.executors.TibannaExecutor method) adjust_filepath() (snakemake.executors.TibannaExecutor method) all_inputfiles() (snakemake.persistence.Persistence method) all_outputfiles() (snakemake.persistence.Persistence method) all_products (snakemake.jobs.GroupJob property) allows_directories (snakemake.remote.AbstractRemoteProvider attribute) AlwaysQuotedFormatter (class in snakemake.utils), [1] AmbiguousRuleException ancient() (in module snakemake.io) AnnotatedString (class in snakemake.io) api_request() (snakemake.remote.EGA.RemoteProvider method) apply_input_function() (snakemake.rules.Rule method) apply_path_modifier() (snakemake.rules.Rule method) apply_wildcards() (in module snakemake.io) archive() (snakemake.dag.DAG method)

archive_conda_env() (snakemake.jobs.Job method) args (snakemake.parser.DecoratorKeywordState attribute) (snakemake.parser.OnError attribute) (snakemake.parser.OnStart attribute) (snakemake.parser.OnSuccess attribute) args() (snakemake.parser.AbstractCmd method) (snakemake.parser.CWL method) (snakemake.parser.Notebook method) (snakemake.parser.Script method) (snakemake.parser.Shell method) (snakemake.parser.Wrapper method) argvquote() (in module snakemake.utils), [1] async_run() (in module snakemake.common) attempt (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) auto_report() (in module snakemake.report) AutoRemoteProvider (class in snakemake.remote) available_cpu_count() (in module snakemake.utils), [1] available_protocols (snakemake.remote.dropbox.RemoteProvider property) (snakemake.remote.EGA.RemoteProvider property) (snakemake.remote.HTTP.RemoteProvider property) (snakemake.remote.NCBI.RemoteProvider property) (snakemake.remote.S3.RemoteProvider property) available_protocols() (snakemake.remote.AbstractRemoteProvider method) AzureFileException

B

b64id (snakemake.jobs.Job property) bash_completion() (in module snakemake) Batch (class in snakemake.dag) bench_record (snakemake.benchmark.BenchmarkTimer attribute) Benchmark (class in snakemake.parser) benchmark (snakemake.jobs.Job property) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) benchmark() (snakemake.workflow.Workflow method) BENCHMARK_INTERVAL (in module snakemake.benchmark) BENCHMARK_INTERVAL_SHORT (in module snakemake.benchmark) benchmark_repeats (snakemake.jobs.Job property) benchmarked() (in module snakemake.benchmark) BenchmarkRecord (class in snakemake.benchmark) BenchmarkTimer (class in snakemake.benchmark)

bfs() (snakemake.dag.DAG method) BLACK (snakemake.logging.ColorizingStreamHandler attribute) block() (snakemake.parser.KeywordState method) block_content() (snakemake.parser.AbstractCmd method) (snakemake.parser.KeywordState method) (snakemake.parser.Localrules method) (snakemake.parser.Module method) (snakemake.parser.Rule method) (snakemake.parser.Ruleorder method) (snakemake.parser.Run method) (snakemake.parser.Subworkflow method) (snakemake.parser.UseRule method) BLUE (snakemake.logging.ColorizingStreamHandler attribute) BOLD_SEQ (snakemake.logging.ColorizingStreamHandler attribute) bucket_exists() (snakemake.remote.S3.S3Helper method) bytesto() (in module snakemake.common)

C

Cache (class in snakemake.parser) cache_job() (snakemake.dag.DAG method) cache_rule() (snakemake.workflow.Workflow method) cached_or_run() (snakemake.executors.CPUExecutor method) CacheMissException calc_resource() (snakemake.scheduler.JobScheduler method) callback (snakemake.executors.DRMAAClusterJob attribute) (snakemake.executors.GenericClusterJob attribute) (snakemake.executors.KubernetesJob attribute) (snakemake.executors.SynchronousClusterJob attribute) (snakemake.executors.TibannaJob attribute) can_color_tty() (snakemake.logging.ColorizingStreamHandler method) cancel() (snakemake.benchmark.DaemonTimer method) (snakemake.benchmark.ScheduledPeriodicTimer method) (snakemake.executors.AbstractExecutor method) (snakemake.executors.ClusterExecutor method) (snakemake.executors.CPUExecutor method) (snakemake.executors.DRMAAExecutor method) (snakemake.executors.GenericClusterExecutor method) (snakemake.executors.KubernetesExecutor method) (snakemake.executors.SynchronousClusterExecutor method) (snakemake.executors.TibannaExecutor method) CandidateGroup (class in snakemake.dag) caption (snakemake.io.ReportObject attribute) Category (class in snakemake.report) category (snakemake.io.ReportObject attribute) change_working_directory() (in module snakemake.executors) check() (snakemake.workflow.Workflow method) check_and_touch_output() (snakemake.dag.DAG method) check_caching() (snakemake.rules.Rule method) check_directory_outputs() (snakemake.dag.DAG method) check_dynamic() (snakemake.dag.DAG method) check_incomplete() (snakemake.dag.DAG method) check_localrules() (snakemake.workflow.Workflow method) check_output() (snakemake.shell.shell class method) check_output_duplicates() (snakemake.rules.Rule method) check_periodic_wildcards() (snakemake.dag.DAG method) check_protected_output() (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) check_response() (snakemake.logging.WMSLogger method) check_source_sizes() (snakemake.workflow.Workflow method) check_wildcards() (snakemake.rules.Rule method) Checkpoint (class in snakemake.checkpoints) (class in snakemake.parser) checkpoint_jobs (snakemake.dag.DAG property) checkpoint_target() (in module snakemake.io) CheckpointJob (class in snakemake.checkpoints) Checkpoints (class in snakemake.checkpoints) checkpoints (snakemake.checkpoints.Checkpoint attribute) checksum (snakemake.remote.EGA.EGAFileInfo attribute) CheckSumMismatchException ChildIOException clean() (snakemake.dag.DAG method) cleanup() (snakemake.dag.DAG method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) (snakemake.logging.Logger method) (snakemake.persistence.Persistence method) (snakemake.shell.shell class method) cleanup_locks() (snakemake.persistence.Persistence method) cleanup_metadata() (snakemake.persistence.Persistence method) cleanup_shadow() (snakemake.persistence.Persistence method) cleanup_workdir() (snakemake.dag.DAG method) clear() (snakemake.io.IOCache method) close() (snakemake.remote.AbstractRemoteObject method)

close_connection() (snakemake.remote.PooledDomainObject method) close_remote() (snakemake.jobs.Job method) close_remote_objects() (snakemake.dag.DAG method) cluster (snakemake.common.Mode attribute) cluster_params() (snakemake.executors.ClusterExecutor method) cluster_wildcards() (snakemake.executors.ClusterExecutor method) ClusterExecutor (class in snakemake.executors) ClusterJobException cmd_exe_quote() (in module snakemake.utils), [1] code (snakemake.report.RuleRecord property) code() (snakemake.persistence.Persistence method) (snakemake.report.ConfigfileRecord method) code_changed() (snakemake.persistence.Persistence method) collect_mtime() (snakemake.io.IOCache method) collect_potential_dependencies() (snakemake.dag.DAG method) colon() (snakemake.parser.KeywordState method) COLOR_SEQ (snakemake.logging.ColorizingStreamHandler attribute) ColorizingStreamHandler (class in snakemake.logging) colors (snakemake.logging.ColorizingStreamHandler attribute) combine_preamble_and_source() (snakemake.script.RustScript method) compare() (snakemake.rules.Ruleorder method) concrete_files (snakemake.workflow.Workflow property) Conda (class in snakemake.parser) conda() (snakemake.workflow.Workflow method) conda_base_path (snakemake.workflow.Workflow property) conda_block_conflicting_envvars (snakemake.shell.shell attribute) conda_cleanup_envs() (snakemake.persistence.Persistence method) conda_env (snakemake.jobs.Job property) (snakemake.rules.Rule property) conda_env_spec (snakemake.jobs.Job property) config (snakemake.workflow.Workflow property) Configfile (class in snakemake.parser) configfile() (snakemake.workflow.Workflow method) ConfigfileRecord (class in snakemake.report) conn_keywords (snakemake.remote.PooledDomainObject property) connection_pool (snakemake.remote.PooledDomainObject property) connection_pools (snakemake.remote.PooledDomainObject attribute) consume() (snakemake.parser.TokenAutomaton method) Container (class in snakemake.parser) container() (snakemake.workflow.Workflow method) container_img (snakemake.jobs.Job property) (snakemake.rules.Rule property) container_img_path (snakemake.jobs.Job property) container_img_url (snakemake.jobs.Job property) containerize() (snakemake.workflow.Workflow method) Containerized (class in snakemake.parser) containerized() (snakemake.workflow.Workflow method) contains_wildcard() (in module snakemake.io) contains_wildcard_constraints() (in module snakemake.io) cores (snakemake.workflow.Workflow property) cpu_time (snakemake.benchmark.BenchmarkRecord attribute) cpu_usages (snakemake.benchmark.BenchmarkRecord attribute) CPUExecutor (class in snakemake.executors) create_conda_envs() (snakemake.dag.DAG method) create_connection() (snakemake.remote.PooledDomainObject method) create_workflow() (snakemake.logging.WMSLogger method) CreateCondaEnvironmentException CreateRuleException cumsum() (in module snakemake.scheduler) current_basedir (snakemake.workflow.Workflow property) cut_traceback() (in module snakemake.exceptions) CWL (class in snakemake.parser) cwl() (in module snakemake.cwl) (snakemake.workflow.Workflow method) CYAN (snakemake.logging.ColorizingStreamHandler attribute) CyclicGraphException

D

d3dag() (snakemake.dag.DAG method) (snakemake.logging.Logger method) DaemonTimer (class in snakemake.benchmark) DAG (class in snakemake.dag) dag (snakemake.jobs.GroupJob property) (snakemake.jobs.Job attribute) dag() (in module snakemake.gui) dag_debug() (snakemake.logging.Logger method) dag_to_cwl() (in module snakemake.cwl) data_uri() (in module snakemake.report) data_uri_from_file() (in module snakemake.report) dataset (snakemake.remote.EGA.EGAFile attribute) dbs_for_options() (snakemake.remote.NCBI.NCBIHelper method) deactivate() (snakemake.io.IOCache method) deactivate_cache() (snakemake.persistence.Persistence method) debug() (snakemake.logging.Logger method) dec_all_methods() (in module snakemake.decorators) decorate() (snakemake.logging.ColorizingStreamHandler method) decorate_end() (snakemake.parser.AbstractCmd method) (snakemake.parser.KeywordState method) decorator (snakemake.parser.DecoratorKeywordState attribute) (snakemake.parser.OnError attribute) (snakemake.parser.OnStart attribute) (snakemake.parser.OnSuccess attribute) DecoratorKeywordState (class in snakemake.parser) dedent (snakemake.parser.Rule property) (snakemake.parser.TokenAutomaton property) (snakemake.parser.UseRule property) default (snakemake.common.Mode attribute) default_dependencies() (snakemake.script.RustScript static method) default_features() (snakemake.script.RustScript static method) default_jobscript (snakemake.executors.ClusterExecutor attribute) default_protocol (snakemake.remote.dropbox.RemoteProvider property) (snakemake.remote.EGA.RemoteProvider property) (snakemake.remote.HTTP.RemoteProvider property) (snakemake.remote.NCBI.RemoteProvider property) (snakemake.remote.S3.RemoteProvider property) default_protocol() (snakemake.remote.AbstractRemoteProvider method)

default_target_rule() (snakemake.workflow.Workflow method) DefaultTarget (class in snakemake.parser) delete_from_bucket() (snakemake.remote.S3.S3Helper method) delete_job() (snakemake.dag.DAG method) delete_omitfrom_jobs() (snakemake.dag.DAG method) dependencies (snakemake.jobs.Job attribute) derived (snakemake.jobs.Reason attribute) dfs() (snakemake.dag.DAG method) directory() (in module snakemake.io) docstring() (snakemake.workflow.Workflow method) DomainObject (class in snakemake.remote) dot() (snakemake.dag.DAG method) download() (snakemake.remote.AbstractRemoteObject method) (snakemake.remote.dropbox.RemoteObject method) (snakemake.remote.EGA.RemoteObject method) (snakemake.remote.HTTP.RemoteObject method) (snakemake.remote.NCBI.RemoteObject method) (snakemake.remote.S3.RemoteObject method) download_from_s3() (snakemake.remote.S3.S3Helper method) download_remote_input() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) downstream_of_omitfrom() (snakemake.dag.DAG method) DRMAAClusterJob (class in snakemake.executors) DRMAAExecutor (class in snakemake.executors) dropbox_file() (snakemake.remote.dropbox.RemoteObject method) DropboxFileException dryrun() (in module snakemake.gui) DryrunExecutor (class in snakemake.executors) DummyRateLimiter (class in snakemake.scheduler) dynamic() (in module snakemake.io) (snakemake.dag.DAG method) dynamic_branch() (snakemake.rules.Rule method) dynamic_input (snakemake.jobs.GroupJob property) (snakemake.jobs.Job attribute) dynamic_output (snakemake.jobs.Job attribute) dynamic_output_jobs (snakemake.dag.DAG property) dynamic_wildcards (snakemake.jobs.Job property)

E

editable (snakemake.script.ScriptBase attribute) effective_indent (snakemake.parser.TokenAutomaton property) EGAFile (class in snakemake.remote.EGA) EGAFileInfo (class in snakemake.remote.EGA) EmbeddedFigure (class in snakemake.report) EmbeddedImage (class in snakemake.report) EmbeddedMixin (class in snakemake.report) emit() (snakemake.logging.ColorizingStreamHandler method) encode_dict() (snakemake.script.JuliaEncoder class method) (snakemake.script.REncoder class method) encode_items() (snakemake.script.JuliaEncoder class method) (snakemake.script.REncoder class method) encode_list() (snakemake.script.JuliaEncoder class method) (snakemake.script.REncoder class method) encode_namedlist() (snakemake.script.JuliaEncoder class method) (snakemake.script.REncoder class method) encode_numeric() (snakemake.script.REncoder class method) encode_positional_items() (snakemake.script.JuliaEncoder class method) encode_value() (snakemake.script.JuliaEncoder class method) (snakemake.script.REncoder class method) end() (snakemake.parser.AbstractCmd method) (snakemake.parser.DecoratorKeywordState method) (snakemake.parser.KeywordState method) (snakemake.parser.Module method) (snakemake.parser.Rule method) (snakemake.parser.Run method) (snakemake.parser.SectionKeywordState method) (snakemake.parser.Subworkflow method) (snakemake.parser.UseRule method) end_func (snakemake.parser.AbstractCmd attribute) (snakemake.parser.CWL attribute) (snakemake.parser.Notebook attribute) (snakemake.parser.Script attribute) (snakemake.parser.Shell attribute) (snakemake.parser.Wrapper attribute) env_modules (snakemake.jobs.Job property) EnvModules (class in snakemake.parser) envmodules() (snakemake.workflow.Workflow method) Envvars (class in snakemake.parser) error() (snakemake.logging.Logger method) (snakemake.parser.TokenAutomaton method) error_callback (snakemake.executors.DRMAAClusterJob attribute) (snakemake.executors.GenericClusterJob attribute) (snakemake.executors.KubernetesJob attribute) (snakemake.executors.SynchronousClusterJob attribute) (snakemake.executors.TibannaJob attribute)

evaluate() (snakemake.script.ScriptBase method) exec_arn (snakemake.executors.TibannaJob attribute) executable() (snakemake.shell.shell class method) execute() (snakemake.workflow.Workflow method) execute_script() (snakemake.script.JuliaScript method) (snakemake.script.PythonScript method) (snakemake.script.RMarkdown method) (snakemake.script.RScript method) (snakemake.script.RustScript method) (snakemake.script.ScriptBase method) executor_error_callback() (snakemake.scheduler.JobScheduler method) existing_output (snakemake.jobs.Job property) existing_remote_input (snakemake.jobs.Job property) existing_remote_output (snakemake.jobs.Job property) exists() (snakemake.remote.AbstractRemoteObject method) (snakemake.remote.dropbox.RemoteObject method) (snakemake.remote.EGA.RemoteObject method) (snakemake.remote.HTTP.RemoteObject method) (snakemake.remote.NCBI.NCBIHelper method) (snakemake.remote.NCBI.RemoteObject method) (snakemake.remote.S3.RemoteObject method) (snakemake.remote.StaticRemoteObjectProxy method) exists_in_bucket() (snakemake.remote.S3.S3Helper method) ExistsDict (class in snakemake.io) exit_gracefully() (snakemake.scheduler.JobScheduler method) expand() (in module snakemake.io) expand_benchmark() (snakemake.rules.Rule method) expand_conda_env() (snakemake.rules.Rule method) expand_dynamic() (snakemake.jobs.Job method) expand_group() (snakemake.rules.Rule method) expand_input() (snakemake.rules.Rule method) expand_log() (snakemake.rules.Rule method) expand_output() (snakemake.rules.Rule method) expand_params() (snakemake.rules.Rule method) expand_resources() (snakemake.rules.Rule method) expanded_output (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) external_jobids() (snakemake.persistence.Persistence method) extract_manifest() (snakemake.script.RustScript static method)

F

fetch_from_ncbi() (snakemake.remote.NCBI.NCBIHelper method) file (snakemake.dag.PotentialDependency attribute) file() (snakemake.remote.AbstractRemoteObject method) file2jobs() (snakemake.dag.DAG method) file_ext (snakemake.remote.NCBI.RemoteObject property) file_stats (snakemake.stats.Stats property) filegraph_dot() (snakemake.dag.DAG method) filename (snakemake.report.FileRecord property) FileRecord (class in snakemake.report) files (snakemake.persistence.Persistence property) files_to_download (snakemake.jobs.Job property) files_to_upload (snakemake.jobs.Job property) finalize() (snakemake.jobs.GroupJob method) find_bash_on_windows() (in module snakemake.utils), [1] find_extension() (in module snakemake.wrapper) finish() (snakemake.dag.DAG method) finished (snakemake.jobs.Reason attribute) finished() (snakemake.dag.DAG method) (snakemake.persistence.Persistence method) finished_jobs (snakemake.dag.DAG property) first_time (snakemake.benchmark.BenchmarkRecord attribute)

flag() (in module snakemake.io) forced (snakemake.jobs.Reason attribute) format() (in module snakemake.utils), [1] format_arg() (snakemake.exceptions.WorkflowError static method) format_dict() (in module snakemake.logging) format_element() (snakemake.utils.SequenceFormatter method), [1] format_error() (in module snakemake.exceptions) format_field() (snakemake.utils.AlwaysQuotedFormatter method) (snakemake.utils.QuotedFormatter method) (snakemake.utils.SequenceFormatter method) format_files() (in module snakemake.jobs) format_job() (snakemake.executors.ClusterExecutor method) format_job_pattern() (snakemake.executors.RealExecutor method) format_percentage() (in module snakemake.logging) format_resource_names() (in module snakemake.logging) format_resources() (in module snakemake.logging) format_tokens() (in module snakemake.parser) format_traceback() (in module snakemake.exceptions) format_wildcards() (in module snakemake.logging) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) FTPFileException

G

Gather (class in snakemake.common) generate_parser_metadata() (in module snakemake) generate_preamble() (snakemake.script.PythonScript static method) (snakemake.script.RScript static method) (snakemake.script.RustScript static method) GenericClusterExecutor (class in snakemake.executors) GenericClusterJob (class in snakemake.executors) get() (snakemake.checkpoints.Checkpoint method) (snakemake.io.Namedlist method) get_additional_args() (snakemake.executors.RealExecutor method) get_appdirs() (in module snakemake.common) get_args() (in module snakemake.gui) get_args_to_use() (snakemake.remote.PooledDomainObject method) get_argument_parser() (in module snakemake) get_batch() (snakemake.dag.Batch method) get_behavior_args() (snakemake.executors.AbstractExecutor method) get_conda_env() (in module snakemake.wrapper) get_connection() (snakemake.remote.PooledDomainObject method) get_container_image() (in module snakemake.common) get_default_kwargs() (snakemake.remote.PooledDomainObject method) get_default_remote_provider_args() (snakemake.executors.AbstractExecutor method) get_default_resources_args() (snakemake.executors.AbstractExecutor method) get_exception_origin() (in module snakemake.exceptions) get_executable() (snakemake.shell.shell class method) get_executor() (snakemake.scheduler.JobScheduler method) get_file_hash() (in module snakemake.common) get_files() (snakemake.remote.EGA.RemoteProvider method) get_flag_value() (in module snakemake.io) get_git_root() (in module snakemake.io) get_git_root_parent_directory() (in module snakemake.io) get_header() (snakemake.benchmark.BenchmarkRecord class method) get_header_item() (snakemake.remote.HTTP.RemoteObject method) get_inventory_parent() (snakemake.remote.AbstractRemoteObject method) get_jobs_or_groups() (snakemake.dag.DAG method) get_jobscript() (snakemake.executors.ClusterExecutor method) get_language() (in module snakemake.script) get_last_stable_version() (in module snakemake.common) get_logfile() (snakemake.logging.Logger method) get_path() (in module snakemake.wrapper) get_preamble() (snakemake.script.JuliaScript method) (snakemake.script.PythonScript method) (snakemake.script.RMarkdown method) (snakemake.script.RScript method) (snakemake.script.RustScript method) (snakemake.script.ScriptBase method)

get_profile_file() (in module snakemake) get_resource_as_string() (in module snakemake.report) get_rule() (snakemake.workflow.Workflow method) get_script() (in module snakemake.wrapper) get_set_resources_args() (snakemake.executors.AbstractExecutor method) get_set_scatter_args() (snakemake.executors.AbstractExecutor method) get_set_threads_args() (snakemake.executors.AbstractExecutor method) get_source() (in module snakemake.script) get_sources() (snakemake.workflow.Workflow method) get_targets() (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) get_uuid() (in module snakemake.common) get_wait_for_files() (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) get_wildcard_len() (snakemake.rules.Rule static method) get_wildcard_names() (in module snakemake.io) get_wildcards() (snakemake.rules.Rule method) git_content() (in module snakemake.io) glob_wildcards() (in module snakemake.io) (snakemake.remote.AbstractRemoteProvider method) global_container() (snakemake.workflow.Workflow method) global_containerized() (snakemake.workflow.Workflow method) global_wildcard_constraints() (snakemake.workflow.Workflow method) GlobalContainer (class in snakemake.parser) GlobalContainerized (class in snakemake.parser) GlobalKeywordState (class in snakemake.parser) globals (snakemake.workflow.Workflow property) GlobalSingularity (class in snakemake.parser) GlobalWildcardConstraints (class in snakemake.parser) GREEN (snakemake.logging.ColorizingStreamHandler attribute) Group (class in snakemake.parser) group (snakemake.jobs.Job property) group() (snakemake.workflow.Workflow method) group_error() (snakemake.logging.Logger method) group_info() (snakemake.logging.Logger method) group_into_chunks() (in module snakemake.common) groupid (snakemake.jobs.GroupJob attribute) GroupJob (class in snakemake.jobs) GroupJobFactory (class in snakemake.jobs) guess_db_options_for_extension() (snakemake.remote.NCBI.NCBIHelper method)

H

handle_job_error() (snakemake.executors.AbstractExecutor method) (snakemake.executors.ClusterExecutor method) (snakemake.executors.CPUExecutor method) (snakemake.executors.RealExecutor method) handle_job_success() (snakemake.executors.AbstractExecutor method) (snakemake.executors.ClusterExecutor method) (snakemake.executors.CPUExecutor method) (snakemake.executors.RealExecutor method) (snakemake.executors.TouchExecutor method) handle_log() (snakemake.dag.DAG method) handle_pipes() (snakemake.dag.DAG method) handle_protected() (snakemake.dag.DAG method) handle_remote() (snakemake.dag.DAG method) (snakemake.executors.TibannaExecutor method)

handle_temp() (snakemake.dag.DAG method) handle_touch() (snakemake.dag.DAG method) handle_with() (snakemake.parser.UseRule method) handler() (snakemake.logging.Logger method) Handover (class in snakemake.parser) handover() (snakemake.workflow.Workflow method) has_wildcards() (snakemake.rules.Rule method) HIGHEST_PRIORITY (snakemake.jobs.Job attribute) host (snakemake.remote.DomainObject property) htmlindex (snakemake.io.ReportObject attribute) HTTPFileException httpr() (snakemake.remote.HTTP.RemoteObject method)

I

icon (snakemake.report.FileRecord property) id (snakemake.remote.EGA.EGAFileInfo attribute) ImproperOutputException ImproperShadowException in_omitfrom() (snakemake.dag.DAG method) in_until() (snakemake.dag.DAG method) Include (class in snakemake.parser) include() (snakemake.workflow.Workflow method) incomplete() (snakemake.persistence.Persistence method) incomplete_external_jobid() (snakemake.dag.DAG method) incomplete_files (snakemake.dag.DAG property) incomplete_output (snakemake.jobs.Reason property) IncompleteCheckpointException IncompleteFilesException indentation() (snakemake.parser.TokenAutomaton method) index() (in module snakemake.gui) info() (snakemake.logging.Logger method) init() (snakemake.dag.DAG method) Input (class in snakemake.parser) input (snakemake.jobs.GroupJob property) (snakemake.jobs.Job attribute) (snakemake.report.RuleRecord property) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) input() (snakemake.persistence.Persistence method) (snakemake.workflow.Workflow method) input_changed() (snakemake.persistence.Persistence method) inputfile() (snakemake.workflow.Workflow method) InputFiles (class in snakemake.io) InputFunctionException inputsize (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) instance() (snakemake.utils.Paramspace method), [1] instance_patterns (snakemake.utils.Paramspace property), [1] inventory() (snakemake.remote.AbstractRemoteObject method) io_in (snakemake.benchmark.BenchmarkRecord attribute) io_out (snakemake.benchmark.BenchmarkRecord attribute) IOCache (class in snakemake.io) IOException IOFile() (in module snakemake.io) IOFileException is_batch_rule() (snakemake.dag.DAG method) is_block_end() (snakemake.parser.AbstractCmd method) (snakemake.parser.KeywordState method) (snakemake.parser.Run method) is_branched (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) is_cached_rule() (snakemake.workflow.Workflow method) is_callable() (in module snakemake.io) is_checkpoint (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) is_colon() (in module snakemake.parser) is_comma() (in module snakemake.parser)

is_comment() (in module snakemake.parser) is_containerized (snakemake.jobs.Job property) is_cwl (snakemake.jobs.Job property) (snakemake.rules.Rule property) is_dedent() (in module snakemake.parser) is_edit_notebook_job() (snakemake.dag.DAG method) is_eof() (in module snakemake.parser) is_final (snakemake.dag.Batch property) is_flagged() (in module snakemake.io) is_git_path() (in module snakemake.wrapper) is_greater() (in module snakemake.parser) is_group() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) is_img (snakemake.report.FileRecord property) is_indent() (in module snakemake.parser) is_local (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) is_local() (in module snakemake.wrapper) (snakemake.workflow.Workflow method) is_local_file() (in module snakemake.common) is_name() (in module snakemake.parser) is_newer() (snakemake.remote.StaticRemoteObjectProxy method) is_newline() (in module snakemake.parser) is_norun (snakemake.jobs.Job property) is_notebook (snakemake.jobs.Job property) (snakemake.rules.Rule property) is_op() (in module snakemake.parser) is_periodic() (snakemake.io.PeriodicityDetector method) is_pipe (snakemake.jobs.Job property) is_producer() (snakemake.rules.Rule method) is_rule() (snakemake.workflow.Workflow method) is_run (snakemake.jobs.Job property) (snakemake.rules.Rule property) is_script (snakemake.jobs.Job property) (snakemake.rules.Rule property) is_script() (in module snakemake.wrapper) is_shadow (snakemake.jobs.Job property) is_shell (snakemake.jobs.Job property) (snakemake.rules.Rule property) is_string() (in module snakemake.parser) is_table (snakemake.report.FileRecord property) is_text (snakemake.report.FileRecord property) is_tty (snakemake.logging.ColorizingStreamHandler property) is_updated (snakemake.jobs.GroupJob property) is_url() (in module snakemake.wrapper) is_valid() (snakemake.jobs.Job method) is_valid_db() (snakemake.remote.NCBI.NCBIHelper method) is_valid_db_request() (snakemake.remote.NCBI.NCBIHelper method) is_vega (snakemake.report.FileRecord property) is_wrapper (snakemake.jobs.Job property) (snakemake.rules.Rule property) items() (snakemake.io.Namedlist method) iter_stdout() (snakemake.shell.shell static method)

J

Job (class in snakemake.jobs) job (snakemake.executors.DRMAAClusterJob attribute) (snakemake.executors.GenericClusterJob attribute) (snakemake.executors.KubernetesJob attribute) (snakemake.executors.SynchronousClusterJob attribute) (snakemake.executors.TibannaJob attribute) job_args_and_prepare() (snakemake.executors.CPUExecutor method) job_error() (snakemake.logging.Logger method) job_finished() (snakemake.logging.Logger method) job_info() (snakemake.logging.Logger method) job_reward() (snakemake.scheduler.JobScheduler method) job_selector_greedy() (snakemake.scheduler.JobScheduler method) job_selector_ilp() (snakemake.scheduler.JobScheduler method) job_to_cwl() (in module snakemake.cwl) job_weight() (snakemake.scheduler.JobScheduler method) JobFactory (class in snakemake.jobs) jobfailed (snakemake.executors.GenericClusterJob attribute) jobfiles() (in module snakemake.jobs) jobfinished (snakemake.executors.GenericClusterJob attribute)

jobid (snakemake.executors.DRMAAClusterJob attribute) (snakemake.executors.GenericClusterJob attribute) (snakemake.executors.KubernetesJob attribute) (snakemake.executors.SynchronousClusterJob attribute) (snakemake.executors.TibannaJob attribute) (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) jobid() (snakemake.dag.DAG method) jobname (snakemake.executors.TibannaJob attribute) JobRecord (class in snakemake.report) jobs (snakemake.dag.DAG property) (snakemake.dag.PotentialDependency attribute) (snakemake.jobs.GroupJob attribute) JobScheduler (class in snakemake.scheduler) jobscript (snakemake.executors.DRMAAClusterJob attribute) (snakemake.executors.GenericClusterJob attribute) (snakemake.executors.KubernetesJob attribute) (snakemake.executors.SynchronousClusterJob attribute) JuliaEncoder (class in snakemake.script) JuliaScript (class in snakemake.script)

K

key_last_modified() (snakemake.remote.S3.S3Helper method) key_size() (snakemake.remote.S3.S3Helper method) keys() (snakemake.io.Namedlist method) keyword (snakemake.parser.Cache property) (snakemake.parser.DefaultTarget property) (snakemake.parser.Envvars property) (snakemake.parser.GlobalContainer property) (snakemake.parser.GlobalContainerized property) (snakemake.parser.GlobalSingularity property) (snakemake.parser.GlobalWildcardConstraints property) (snakemake.parser.KeywordState property) (snakemake.parser.ModuleMetaWrapper property) (snakemake.parser.ModuleReplacePrefix property) (snakemake.parser.ModuleSkipValidation property) (snakemake.parser.Pepfile property) (snakemake.parser.Singularity property) (snakemake.parser.WildcardConstraints property)

KeywordState (class in snakemake.parser) kill() (snakemake.shell.shell class method) known (snakemake.dag.PotentialDependency attribute) kubejob (snakemake.executors.KubernetesJob attribute) KubernetesExecutor (class in snakemake.executors) KubernetesJob (class in snakemake.executors)

L

lchmod() (in module snakemake.io) level_bfs() (snakemake.dag.DAG method) limit() (in module snakemake.io) linecount() (in module snakemake.utils), [1] lineno() (in module snakemake.parser) lint() (snakemake.workflow.Workflow method) list (snakemake.remote.dropbox.RemoteObject property) (snakemake.remote.HTTP.RemoteObject property) (snakemake.remote.NCBI.RemoteObject property) (snakemake.remote.S3.RemoteObject property) list() (snakemake.remote.AbstractRemoteObject method) list_keys() (snakemake.remote.S3.S3Helper method) list_resources() (snakemake.workflow.Workflow method) list_rules() (snakemake.workflow.Workflow method) list_untracked() (snakemake.dag.DAG method) listfiles() (in module snakemake.utils), [1] load_configfile() (in module snakemake.io) local() (in module snakemake.io) (snakemake.io.Mtime method) local_file() (snakemake.remote.AbstractRemoteObject method) local_input (snakemake.jobs.Job property) local_needrun_jobs (snakemake.dag.DAG property) local_or_remote() (snakemake.io.Mtime method) local_output (snakemake.jobs.Job property) local_path (snakemake.remote.DomainObject property) (snakemake.script.ScriptBase property) local_touch_or_create() (snakemake.remote.AbstractRemoteObject method) Localrules (class in snakemake.parser)

localrules() (snakemake.workflow.Workflow method) location() (snakemake.logging.Logger method) lock() (snakemake.persistence.Persistence method) lock_warn_only() (snakemake.persistence.Persistence method) locked (snakemake.persistence.Persistence property) Log (class in snakemake.io) (class in snakemake.parser) log (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) log() (in module snakemake.gui) (snakemake.persistence.Persistence method) (snakemake.workflow.Workflow method) log_error() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) log_fmt_shell() (snakemake.script.Snakemake method) log_handler() (snakemake.logging.SlackLogger method) (snakemake.logging.WMSLogger method) log_info() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) log_location() (in module snakemake.common) log_verbose_traceback() (in module snakemake.exceptions) logfile_hint() (snakemake.logging.Logger method) Logger (class in snakemake.logging) lutime() (in module snakemake.io)

M

MAGENTA (snakemake.logging.ColorizingStreamHandler attribute) main() (in module snakemake) make_tibanna_input() (snakemake.executors.TibannaExecutor method) makedirs() (in module snakemake.utils), [1] mark_finished() (snakemake.jobs.Reason method) match() (snakemake.output_index.OutputIndex method) max_pss (snakemake.benchmark.BenchmarkRecord attribute) max_rss (snakemake.benchmark.BenchmarkRecord attribute) max_uss (snakemake.benchmark.BenchmarkRecord attribute) max_vms (snakemake.benchmark.BenchmarkRecord attribute) merge() (snakemake.dag.CandidateGroup method) (snakemake.jobs.GroupJob method) Message (class in snakemake.parser) message (snakemake.jobs.Job property) message() (snakemake.workflow.Workflow method) messages (snakemake.exceptions.RuleException property) metadata() (snakemake.persistence.Persistence method) migrate_v1_to_v2() (snakemake.persistence.Persistence method) mime_from_file() (in module snakemake.report) min_version() (in module snakemake.utils), [1] missing_input (snakemake.jobs.Job property) missing_output (snakemake.jobs.Reason property) missing_output() (snakemake.jobs.Job method) missing_remote_input (snakemake.jobs.Job property) missing_remote_output (snakemake.jobs.Job property) missing_temp() (snakemake.dag.DAG method) MissingInputException MissingOutputException MissingRuleException Mode (class in snakemake.common) modifier (snakemake.workflow.Workflow property) module snakemake snakemake.benchmark snakemake.checkpoints snakemake.common snakemake.cwl snakemake.dag snakemake.decorators snakemake.exceptions snakemake.executors snakemake.gui snakemake.io snakemake.jobs snakemake.logging snakemake.output_index snakemake.parser snakemake.persistence snakemake.remote snakemake.remote.dropbox snakemake.remote.EGA snakemake.remote.HTTP snakemake.remote.NCBI snakemake.remote.S3 snakemake.report snakemake.rules snakemake.scheduler snakemake.script snakemake.shell snakemake.stats snakemake.utils, [1] snakemake.workflow snakemake.wrapper

Module (class in snakemake.parser) module() (snakemake.workflow.Workflow method) ModuleConfig (class in snakemake.parser) ModuleKeywordState (class in snakemake.parser) ModuleMetaWrapper (class in snakemake.parser) ModulePrefix (class in snakemake.parser) ModuleReplacePrefix (class in snakemake.parser) ModuleSkipValidation (class in snakemake.parser) ModuleSnakefile (class in snakemake.parser) Mtime (class in snakemake.io) mtime() (snakemake.remote.AbstractRemoteObject method) (snakemake.remote.dropbox.RemoteObject method) (snakemake.remote.EGA.RemoteObject method) (snakemake.remote.HTTP.RemoteObject method) (snakemake.remote.NCBI.NCBIHelper method) (snakemake.remote.NCBI.RemoteObject method) (snakemake.remote.S3.RemoteObject method) (snakemake.remote.StaticRemoteObjectProxy method) mtime_inventory() (snakemake.io.IOCache method) multiext() (in module snakemake.io)

N

Name (class in snakemake.parser) name (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) (snakemake.remote.DomainObject property) (snakemake.remote.dropbox.RemoteObject property) (snakemake.remote.S3.RemoteObject property) (snakemake.report.FileRecord property) name() (snakemake.parser.Module method) (snakemake.parser.Rule method) (snakemake.parser.Subworkflow method) (snakemake.remote.AbstractRemoteObject method) (snakemake.workflow.Workflow method) Namedlist (class in snakemake.io) NCBIFileException NCBIHelper (class in snakemake.remote.NCBI) needrun() (snakemake.dag.DAG method) needrun_jobs (snakemake.dag.DAG property) needs_singularity (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property)

new() (snakemake.jobs.GroupJobFactory method) (snakemake.jobs.JobFactory method) new_from() (snakemake.io.AnnotatedString method) new_job() (snakemake.dag.DAG method) new_wildcards() (snakemake.dag.DAG method) newversion_files (snakemake.dag.DAG property) nodes (snakemake.workflow.Workflow property) noio (snakemake.jobs.Reason attribute) noneedrun_finished() (snakemake.dag.DAG method) noop() (snakemake.persistence.Persistence method) nooutput (snakemake.jobs.Reason attribute) NoRulesException norun() (snakemake.workflow.Workflow method) not_iterable() (in module snakemake.io) Notebook (class in snakemake.parser) notebook() (snakemake.workflow.Workflow method) num_if_possible() (in module snakemake.common)

O

obj_cache (snakemake.jobs.GroupJob attribute) (snakemake.jobs.Job attribute) omitfrom_jobs() (snakemake.dag.DAG method) OnError (class in snakemake.parser) onerror() (snakemake.workflow.Workflow method) OnStart (class in snakemake.parser) onstart() (snakemake.workflow.Workflow method) OnSuccess (class in snakemake.parser) onsuccess() (snakemake.workflow.Workflow method) open_jobs (snakemake.scheduler.JobScheduler property) options_for_db_and_extension() (snakemake.remote.NCBI.NCBIHelper method) os_sync() (in module snakemake.utils), [1] Output (class in snakemake.parser)

output (snakemake.checkpoints.CheckpointJob attribute) (snakemake.jobs.GroupJob property) (snakemake.jobs.Job attribute) (snakemake.report.RuleRecord property) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) output() (snakemake.workflow.Workflow method) output_mintime (snakemake.jobs.Job property) OutputFiles (class in snakemake.io) OutputIndex (class in snakemake.output_index) outputs_older_than_script_or_notebook() (snakemake.jobs.Job method) overall_runtime (snakemake.stats.Stats property) overwrite_block_content() (snakemake.parser.AbstractCmd method) overwrite_cmd (snakemake.parser.AbstractCmd attribute)

P

Params (class in snakemake.io) (class in snakemake.parser) params (snakemake.jobs.Job property) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) params() (snakemake.persistence.Persistence method) (snakemake.workflow.Workflow method) params_changed() (snakemake.persistence.Persistence method) Paramspace (class in snakemake.utils), [1] parse() (in module snakemake.parser) parse_accession_str() (snakemake.remote.NCBI.NCBIHelper method) parse_batch() (in module snakemake) parse_config() (in module snakemake) parse_group_components() (in module snakemake) parse_groups() (in module snakemake) parse_key_value_arg() (in module snakemake) parse_set_ints() (in module snakemake) parse_set_resources() (in module snakemake) parse_set_scatter() (in module snakemake) parse_set_threads() (in module snakemake) parse_uri() (in module snakemake.common) parts (snakemake.remote.EGA.RemoteObject property) path (snakemake.remote.EGA.EGAFile attribute) path_prefix (snakemake.remote.DomainObject property) path_remainder (snakemake.remote.DomainObject property) patterns (snakemake.io.ReportObject attribute) Pepfile (class in snakemake.parser) Pepschema (class in snakemake.parser) pepschema() (snakemake.workflow.Workflow method) PeriodicityDetector (class in snakemake.io) PeriodicWildcardError Persistence (class in snakemake.persistence) pickle_code() (in module snakemake.persistence) pid (snakemake.benchmark.BenchmarkTimer attribute) pipe (snakemake.jobs.Reason attribute) pipe() (in module snakemake.io) png_content (snakemake.report.FileRecord property) PooledDomainObject (class in snakemake.remote) port (snakemake.remote.DomainObject property) postprocess() (snakemake.dag.DAG method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method)

PotentialDependency (class in snakemake.dag) prefix (snakemake.parser.KeywordState attribute) (snakemake.parser.ModuleKeywordState attribute) (snakemake.parser.SubworkflowKeywordState attribute) prefix() (snakemake.shell.shell class method) prepare() (snakemake.jobs.Job method) prev_time (snakemake.benchmark.BenchmarkRecord attribute) print_benchmark_records() (in module snakemake.benchmark) print_cluster_job_error() (snakemake.executors.ClusterExecutor method) print_exception() (in module snakemake.exceptions) print_job_error() (snakemake.executors.AbstractExecutor method) printcache() (snakemake.executors.DryrunExecutor method) printjob() (snakemake.executors.AbstractExecutor method) (snakemake.executors.DryrunExecutor method) Priority (class in snakemake.parser) priority (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) priority() (snakemake.dag.DAG method) (snakemake.workflow.Workflow method) process (snakemake.executors.SynchronousClusterJob attribute) procs (snakemake.benchmark.BenchmarkTimer attribute) products (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) (snakemake.rules.Rule property) progress() (in module snakemake.gui) (snakemake.logging.Logger method) (snakemake.scheduler.JobScheduler method) properties() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) protected() (in module snakemake.io) protected_output (snakemake.jobs.Job attribute) ProtectedOutputException protocol_mapping (snakemake.remote.AutoRemoteProvider property) pull_container_imgs() (snakemake.dag.DAG method) Python (class in snakemake.parser) python() (snakemake.parser.Python method) PythonScript (class in snakemake.script)

Q

QuotedFormatter (class in snakemake.utils), [1]

R

R() (in module snakemake.utils), [1] read_job_properties() (in module snakemake.utils), [1] ready_jobs (snakemake.dag.DAG property) RealExecutor (class in snakemake.executors) Reason (class in snakemake.jobs) reason() (snakemake.dag.DAG method) RED (snakemake.logging.ColorizingStreamHandler attribute) regex() (in module snakemake.io) register() (in module snakemake.gui) (snakemake.checkpoints.Checkpoints method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) register_envvars() (snakemake.workflow.Workflow method) register_job() (snakemake.executors.GenericClusterExecutor method) (snakemake.executors.RealExecutor method) register_running() (snakemake.dag.DAG method) register_secret() (snakemake.executors.KubernetesExecutor method) register_wildcards() (snakemake.rules.Rule method) remaining_jobs (snakemake.scheduler.JobScheduler property) remote() (snakemake.io.Mtime method) (snakemake.remote.AbstractRemoteObject method) (snakemake.remote.AbstractRemoteProvider method) (snakemake.remote.AutoRemoteProvider method) (snakemake.remote.HTTP.RemoteProvider method) remote_file() (snakemake.remote.AbstractRemoteObject method) remote_input (snakemake.jobs.Job property) remote_input_newer_than_local (snakemake.jobs.Job property) remote_input_older_than_local (snakemake.jobs.Job property) remote_interface() (snakemake.remote.AbstractRemoteProvider method) (snakemake.remote.dropbox.RemoteProvider method) (snakemake.remote.NCBI.RemoteProvider method) (snakemake.remote.S3.RemoteProvider method) remote_output (snakemake.jobs.Job property) remote_output_newer_than_local (snakemake.jobs.Job property) remote_output_older_than_local (snakemake.jobs.Job property) remote_path (snakemake.remote.DomainObject property) RemoteFileException RemoteObject (class in snakemake.remote.dropbox) (class in snakemake.remote.EGA) (class in snakemake.remote.HTTP) (class in snakemake.remote.NCBI) (class in snakemake.remote.S3) RemoteProvider (class in snakemake.remote.dropbox) (class in snakemake.remote.EGA) (class in snakemake.remote.HTTP) (class in snakemake.remote.NCBI) (class in snakemake.remote.S3) remove() (in module snakemake.io) (snakemake.remote.AbstractRemoteObject method) remove_existing_output() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) remove_logfile() (snakemake.logging.Logger method) remove_prefix() (snakemake.executors.TibannaExecutor method) REncoder (class in snakemake.script) render() (snakemake.report.FileRecord method) repeat() (in module snakemake.io) replace_job() (snakemake.dag.DAG method) Report (class in snakemake.parser) report() (in module snakemake.io) (in module snakemake.report) (in module snakemake.utils), [1] (snakemake.workflow.Workflow method) report_job_end() (snakemake.stats.Stats method) report_job_start() (snakemake.stats.Stats method)

ReportObject (class in snakemake.io) requested_files() (snakemake.dag.DAG method) required_by_job() (snakemake.scheduler.JobScheduler method) reset_params_and_resources() (snakemake.jobs.AbstractJob method) (snakemake.jobs.GroupJob method) (snakemake.jobs.Job method) RESET_SEQ (snakemake.logging.ColorizingStreamHandler attribute) Resources (class in snakemake.io) (class in snakemake.parser) resources (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) resources() (snakemake.workflow.Workflow method) resources_info() (snakemake.logging.Logger method) restart_times (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) RMarkdown (class in snakemake.script) RScript (class in snakemake.script) Rule (class in snakemake.parser) (class in snakemake.rules) rule (snakemake.checkpoints.Checkpoint attribute) (snakemake.checkpoints.CheckpointJob attribute) (snakemake.jobs.Job attribute) rule() (snakemake.persistence.Persistence method) (snakemake.workflow.Workflow method) rule2job() (snakemake.dag.DAG method) rule_dot() (snakemake.dag.DAG method) rule_dot2() (snakemake.dag.DAG method) rule_info() (snakemake.logging.Logger method) rule_prefix() (snakemake.executors.AbstractExecutor method) rule_stats (snakemake.stats.Stats property) rule_weight() (snakemake.scheduler.JobScheduler method) RuleException rulegraph_d3_spec() (in module snakemake.report) RuleKeywordState (class in snakemake.parser) Ruleorder (class in snakemake.parser) (class in snakemake.rules) ruleorder() (snakemake.workflow.Workflow method) RuleProxy (class in snakemake.rules) RuleRecord (class in snakemake.report) Rules (class in snakemake.common) rules (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) (snakemake.workflow.Workflow property) Run (class in snakemake.parser) run() (in module snakemake.gui) (snakemake.benchmark.DaemonTimer method) (snakemake.executors.AbstractExecutor method) (snakemake.executors.CPUExecutor method) (snakemake.executors.DRMAAExecutor method) (snakemake.executors.GenericClusterExecutor method) (snakemake.executors.KubernetesExecutor method) (snakemake.executors.SynchronousClusterExecutor method) (snakemake.executors.TibannaExecutor method) (snakemake.executors.TouchExecutor method) (snakemake.report.EmbeddedMixin method) (snakemake.scheduler.JobScheduler method) (snakemake.workflow.Workflow method) run_group_job() (snakemake.executors.CPUExecutor method) run_info() (snakemake.logging.Logger method) run_jobs() (snakemake.executors.AbstractExecutor method) run_single_job() (snakemake.executors.CPUExecutor method) run_snakemake() (in module snakemake.gui) run_wrapper() (in module snakemake.executors) running_time (snakemake.benchmark.BenchmarkRecord attribute) RustScript (class in snakemake.script)

S

s3_bucket (snakemake.remote.S3.RemoteObject property) s3_create_stub() (snakemake.remote.S3.RemoteObject method) s3_key (snakemake.remote.S3.RemoteObject property) S3FileException S3Helper (class in snakemake.remote.S3) safe_delete_pod() (snakemake.executors.KubernetesExecutor method) Scatter (class in snakemake.common) Scattergather (class in snakemake.parser) scattergather() (snakemake.workflow.Workflow method) schedule() (snakemake.scheduler.JobScheduler method) ScheduledPeriodicTimer (class in snakemake.benchmark) Script (class in snakemake.parser) script() (in module snakemake.script) (snakemake.workflow.Workflow method) ScriptBase (class in snakemake.script) search() (snakemake.remote.NCBI.NCBIHelper method) (snakemake.remote.NCBI.RemoteProvider method) SectionKeywordState (class in snakemake.parser) SequenceFormatter (class in snakemake.utils), [1] service_info() (snakemake.logging.WMSLogger method) set_args() (in module snakemake.gui) set_input() (snakemake.rules.Rule method) set_level() (snakemake.logging.Logger method) set_log() (snakemake.rules.Rule method) set_output() (snakemake.rules.Rule method) set_params() (snakemake.rules.Rule method) set_pepfile() (snakemake.workflow.Workflow method) set_stream_handler() (snakemake.logging.Logger method) set_until_jobs() (snakemake.dag.DAG method) set_wildcard_constraints() (snakemake.rules.Rule method) setup_logfile() (snakemake.logging.Logger method) setup_logger() (in module snakemake.logging) SFTPFileException Shadow (class in snakemake.parser) shadow() (snakemake.workflow.Workflow method) shadow_dir (snakemake.jobs.Job attribute) shadowed_path() (snakemake.jobs.Job method) Shell (class in snakemake.parser) shell (class in snakemake.shell) shellcmd (snakemake.jobs.Job property) shellcmd() (snakemake.logging.Logger method) (snakemake.persistence.Persistence method) (snakemake.workflow.Workflow method) shutdown() (snakemake.executors.AbstractExecutor method) (snakemake.executors.ClusterExecutor method) (snakemake.executors.CPUExecutor method) (snakemake.executors.DRMAAExecutor method) (snakemake.executors.KubernetesExecutor method) (snakemake.executors.TibannaExecutor method) simplify_path() (in module snakemake.utils), [1] Singularity (class in snakemake.parser) size (snakemake.io.InputFiles property) (snakemake.remote.EGA.EGAFileInfo attribute) size() (snakemake.remote.AbstractRemoteObject method) (snakemake.remote.dropbox.RemoteObject method) (snakemake.remote.EGA.RemoteObject method) (snakemake.remote.HTTP.RemoteObject method) (snakemake.remote.NCBI.NCBIHelper method) (snakemake.remote.NCBI.RemoteObject method) (snakemake.remote.S3.RemoteObject method) size_mb (snakemake.io.InputFiles property) SlackLogger (class in snakemake.logging) sleep() (in module snakemake.executors) smart_join() (in module snakemake.common) Snakefile (class in snakemake.parser) snakefile (snakemake.workflow.Subworkflow property) (snakemake.workflow.Workflow property) snakemake module Snakemake (class in snakemake.script) snakemake() (in module snakemake), [1] snakemake.benchmark module snakemake.checkpoints module snakemake.common module snakemake.cwl module snakemake.dag module snakemake.decorators module snakemake.exceptions module snakemake.executors module snakemake.gui module snakemake.io module snakemake.jobs module snakemake.logging module snakemake.output_index module snakemake.parser module

snakemake.persistence module snakemake.remote module snakemake.remote.dropbox module snakemake.remote.EGA module snakemake.remote.HTTP module snakemake.remote.NCBI module snakemake.remote.S3 module snakemake.report module snakemake.rules module snakemake.scheduler module snakemake.script module snakemake.shell module snakemake.stats module snakemake.utils module, [1] snakemake.workflow module snakemake.wrapper module source_path() (snakemake.workflow.Workflow method) SourceFileError spawn_job() (snakemake.executors.CPUExecutor method) SpawnedJobError specialize_rule() (snakemake.dag.DAG method) split_filename() (snakemake.executors.TibannaExecutor method) split_git_path() (in module snakemake.io) srcdir() (in module snakemake.workflow) start() (snakemake.benchmark.ScheduledPeriodicTimer method) (snakemake.parser.AbstractCmd method) (snakemake.parser.Checkpoint method) (snakemake.parser.DecoratorKeywordState method) (snakemake.parser.GlobalKeywordState method) (snakemake.parser.Rule method) (snakemake.parser.RuleKeywordState method) (snakemake.parser.Run method) (snakemake.parser.SectionKeywordState method) start_func (snakemake.parser.AbstractCmd attribute) (snakemake.parser.CWL attribute) (snakemake.parser.Notebook attribute) (snakemake.parser.Script attribute) (snakemake.parser.Shell attribute) (snakemake.parser.Wrapper attribute) started() (snakemake.persistence.Persistence method) state_as() (snakemake.parser.UseRule method) state_from() (snakemake.parser.UseRule method) state_keyword_rule() (snakemake.parser.UseRule method) state_modifier() (snakemake.parser.UseRule method) state_rules_comma_or_end() (snakemake.parser.UseRule method) state_rules_end() (snakemake.parser.UseRule method) state_rules_rule() (snakemake.parser.UseRule method) state_with() (snakemake.parser.UseRule method) StaticRemoteObjectProxy (class in snakemake.remote) Stats (class in snakemake.stats) stats (snakemake.scheduler.JobScheduler property) stats() (snakemake.dag.DAG method) status (snakemake.remote.EGA.EGAFileInfo attribute) status() (in module snakemake.gui) StopAutomaton strip_prefix() (in module snakemake.common) strip_re() (in module snakemake.script) strip_wildcard_constraints() (in module snakemake.io) subautomata (snakemake.parser.Module attribute) (snakemake.parser.Python attribute) (snakemake.parser.Rule attribute) (snakemake.parser.Subworkflow attribute) (snakemake.parser.TokenAutomaton attribute) (snakemake.parser.UseRule attribute) subautomaton() (snakemake.parser.TokenAutomaton method) subcategory (snakemake.io.ReportObject attribute) subprocess (snakemake.common.Mode attribute) Subworkflow (class in snakemake.parser) (class in snakemake.workflow) subworkflow() (snakemake.workflow.Workflow method) subworkflow_input (snakemake.jobs.Job attribute) SubworkflowConfigfile (class in snakemake.parser) SubworkflowKeywordState (class in snakemake.parser) subworkflows (snakemake.workflow.Workflow property) SubworkflowSnakefile (class in snakemake.parser) SubworkflowWorkdir (class in snakemake.parser) suffix() (snakemake.shell.shell class method) summary() (snakemake.dag.DAG method) supports_default (snakemake.remote.AbstractRemoteProvider attribute) (snakemake.remote.S3.RemoteProvider attribute) SynchronousClusterExecutor (class in snakemake.executors) SynchronousClusterJob (class in snakemake.executors)

T

target (snakemake.jobs.Reason attribute) target() (snakemake.workflow.Subworkflow method) targetfile (snakemake.jobs.Job attribute) targets() (in module snakemake.gui) (snakemake.workflow.Subworkflow method) TBDString (class in snakemake.common) temp() (in module snakemake.io) temp_input() (snakemake.dag.DAG method) temp_output (snakemake.jobs.Job attribute) temp_size() (snakemake.dag.DAG method) temporary() (in module snakemake.io) TerminatedException text_handler() (snakemake.logging.Logger method) Threads (class in snakemake.parser)

threads (snakemake.jobs.GroupJob property) (snakemake.jobs.Job property) threads() (snakemake.workflow.Workflow method) TibannaExecutor (class in snakemake.executors) TibannaJob (class in snakemake.executors) tmpdir (snakemake.executors.ClusterExecutor property) to_json() (snakemake.stats.Stats method) to_tsv() (snakemake.benchmark.BenchmarkRecord method) token (snakemake.remote.EGA.RemoteProvider property) TokenAutomaton (class in snakemake.parser) toposorted (snakemake.jobs.GroupJob attribute) touch() (in module snakemake.io) touch_output (snakemake.jobs.Job attribute) TouchExecutor (class in snakemake.executors)

U

UnexpectedOutputException Unformattable (class in snakemake.utils) unique_input (snakemake.jobs.Job property) UnknownRuleException unlock() (snakemake.persistence.Persistence method) unpack() (in module snakemake.io) unparse_config() (in module snakemake) unregister_secret() (snakemake.executors.KubernetesExecutor method) unshadow_output() (snakemake.dag.DAG method) until_jobs() (snakemake.dag.DAG method) update() (snakemake.dag.DAG method) update_() (snakemake.dag.DAG method) update_checkpoint_dependencies() (snakemake.dag.DAG method) update_checkpoint_outputs() (snakemake.dag.DAG method) update_config() (in module snakemake.utils), [1] update_dynamic() (snakemake.dag.DAG method) update_groups() (snakemake.dag.DAG method)

update_jobids() (snakemake.dag.DAG method) update_needrun() (snakemake.dag.DAG method) update_output_index() (snakemake.dag.DAG method) update_priority() (snakemake.dag.DAG method) update_ready() (snakemake.dag.DAG method) update_wildcard_constraints() (in module snakemake.io) (snakemake.rules.Rule method) updated() (snakemake.jobs.Job method) updated_input (snakemake.jobs.Reason property) updated_input_run (snakemake.jobs.Reason property) upload() (snakemake.remote.AbstractRemoteObject method) (snakemake.remote.dropbox.RemoteObject method) (snakemake.remote.HTTP.RemoteObject method) (snakemake.remote.NCBI.RemoteObject method) (snakemake.remote.S3.RemoteObject method) upload_to_s3() (snakemake.remote.S3.S3Helper method) UseRule (class in snakemake.parser) userule() (snakemake.workflow.Workflow method)

V

valid_dbs (snakemake.remote.NCBI.NCBIHelper property) valid_extensions (snakemake.remote.NCBI.NCBIHelper property) validate() (in module snakemake.utils), [1] Version (class in snakemake.parser)

version (snakemake.remote.NCBI.RemoteObject property) (snakemake.rules.Rule property) version() (snakemake.persistence.Persistence method) (snakemake.workflow.Workflow method) version_changed() (snakemake.persistence.Persistence method)

W

wait_for_files() (in module snakemake.io) warning() (snakemake.logging.Logger method) WebDAVFileException WHITE (snakemake.logging.ColorizingStreamHandler attribute) wildcard_constraints (snakemake.rules.Rule property) wildcard_constraints() (snakemake.workflow.Workflow method) wildcard_names (snakemake.rules.Rule property) wildcard_pattern (snakemake.utils.Paramspace property), [1] WildcardConstraints (class in snakemake.parser) WildcardError Wildcards (class in snakemake.io) wildcards (snakemake.jobs.Job attribute) wildcards_dict (snakemake.jobs.Job attribute) win_command_prefix() (snakemake.shell.shell class method) WMSLogger (class in snakemake.logging) work() (snakemake.benchmark.BenchmarkTimer method) (snakemake.benchmark.ScheduledPeriodicTimer method)

Workdir (class in snakemake.parser) workdir (snakemake.workflow.Subworkflow property) workdir() (snakemake.workflow.Workflow method) Workflow (class in snakemake.workflow) WorkflowError Wrapper (class in snakemake.parser) wrapper() (in module snakemake.wrapper) (snakemake.workflow.Workflow method) write_benchmark_records() (in module snakemake.benchmark) write_jobscript() (snakemake.executors.ClusterExecutor method) write_script() (snakemake.script.JuliaScript method) (snakemake.script.PythonScript method) (snakemake.script.RMarkdown method) (snakemake.script.RScript method) (snakemake.script.RustScript method) (snakemake.script.ScriptBase method)

X

XRootDFileException

Y

YELLOW (snakemake.logging.ColorizingStreamHandler attribute)

yield_indent() (snakemake.parser.KeywordState method)