Index

_

__init__() (snakemake.settings.enums.ChangeType method) (snakemake.settings.enums.CondaCleanupPkgs method) (snakemake.settings.enums.Quietness method) (snakemake.settings.enums.RerunTrigger method) (snakemake.settings.enums.StrictDagEvaluation method)

A

abspath() (snakemake.sourcecache.LocalSourceFile method) add() (snakemake.rules.Ruleorder method) add_argument() (snakemake.common.argparse.ArgumentGroup method) (snakemake.common.argparse.ArgumentParser method) add_argument_group() (snakemake.common.argparse.ArgumentParser method) address (snakemake.deployment.conda.Env property) address_argument (snakemake.deployment.conda.Env property) ALL (snakemake.settings.enums.Quietness attribute) AlwaysQuotedFormatter (class in snakemake.utils) AmbiguousRuleException anchor() (snakemake.script.ReportHref method) ancient() (in module snakemake.io) AnnotatedString (class in snakemake.io) AnnotatedStringInterface (class in snakemake.io) apply_default_storage() (snakemake.path_modifier.PathModifier method) apply_func() (snakemake.ioutils.lookup.DpathWildcardHandler method) (snakemake.ioutils.lookup.QueryWildcardHandler method) (snakemake.ioutils.lookup.WildcardHandlerBase method) apply_input_function() (snakemake.rules.Rule method) apply_modifier() (snakemake.ruleinfo.RuleInfo method)

apply_path_modifier() (snakemake.rules.Rule method) apply_wildcards() (in module snakemake.io) (snakemake.deployment.conda.CondaEnvDirSpec method) (snakemake.deployment.conda.CondaEnvFileSpec method) (snakemake.deployment.conda.CondaEnvNameSpec method) (snakemake.deployment.conda.CondaEnvSpec method) archive_file (snakemake.deployment.conda.Env property) args (snakemake.resources.DefaultResources property) ArgumentDefaultsHelpFormatter (class in snakemake.common.argparse) ArgumentGroup (class in snakemake.common.argparse) ArgumentParser (class in snakemake.common.argparse) argvquote() (in module snakemake.utils) Asset (class in snakemake.assets) AssetDownloadError Assets (class in snakemake.assets) async_run() (in module snakemake.common) ATTRIBUTE (snakemake.ioutils.rule_items_proxy.KeyKind attribute) AttributeGuard (class in snakemake.io) available_cpu_count() (in module snakemake.utils) AzureFileException

B

bare_defaults (snakemake.resources.DefaultResources attribute) base_path() (snakemake.assets.Assets class method) BashEncoder (class in snakemake.script) BashScript (class in snakemake.script) basic_layered() (snakemake.resources.GroupResources class method) before_update() (in module snakemake.ioflags) bench_record (snakemake.benchmark.BenchmarkTimer attribute) benchmark (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) BENCHMARK_INTERVAL (in module snakemake.benchmark)

BENCHMARK_INTERVAL_SHORT (in module snakemake.benchmark) benchmarked() (in module snakemake.benchmark) BenchmarkRecord (class in snakemake.benchmark) BenchmarkTimer (class in snakemake.benchmark) bin_path() (snakemake.deployment.conda.Conda method) BLACK (snakemake.logging.ColorizingTextHandler attribute) BLUE (snakemake.logging.ColorizingTextHandler attribute) BOLD_SEQ (snakemake.logging.ColorizingTextHandler attribute) branch() (in module snakemake.ioutils.branch) bytesto() (in module snakemake.common)

C

cache (snakemake.deployment.conda.CondaCleanupMode attribute) CACHE (snakemake.settings.enums.CondaCleanupPkgs attribute) cache_whitelist (snakemake.sourcecache.SourceCache attribute) CacheMissException can_color_tty() (snakemake.logging.ColorizingTextHandler method) cancel() (snakemake.benchmark.DaemonTimer method) (snakemake.benchmark.ScheduledPeriodicTimer method) (snakemake.executors.dryrun.Executor method) (snakemake.executors.touch.Executor method) caption (snakemake.io.ReportObject attribute) category (snakemake.io.ReportObject attribute) change_back() (snakemake.common.workdir_handler.WorkdirHandler method) change_to() (snakemake.common.workdir_handler.WorkdirHandler method) change_working_directory() (in module snakemake.executors) ChangeType (class in snakemake.settings.enums), [1] check() (snakemake.deployment.conda.CondaEnvDirSpec method) (snakemake.deployment.conda.CondaEnvFileSpec method) (snakemake.deployment.conda.CondaEnvNameSpec method) (snakemake.deployment.conda.CondaEnvSpec method) (snakemake.deployment.singularity.Singularity method) check_caching() (snakemake.rules.Rule method) check_is_file_based() (snakemake.deployment.conda.Env method) check_output() (snakemake.shell.shell class method) check_output_duplicates() (snakemake.rules.Rule method) check_template_output() (in module snakemake.template_rendering) check_wildcards() (snakemake.rules.Rule method) Checkpoint (class in snakemake.checkpoints) checkpoint_target() (in module snakemake.io) CheckpointJob (class in snakemake.checkpoints) Checkpoints (class in snakemake.checkpoints) checkpoints (snakemake.checkpoints.Checkpoint attribute) CheckSumMismatchException child_path() (snakemake.script.ReportHref method) ChildIOException cleanup() (snakemake.shell.shell class method) cleanup_logfile() (snakemake.logging.LoggerManager method) clear() (snakemake.io.IOCache method) CliException ClusterJobException cmd_exe_quote() (in module snakemake.utils) CODE (snakemake.settings.enums.ChangeType attribute) (snakemake.settings.enums.RerunTrigger attribute) collect_mtime() (snakemake.io.IOCache method) COLOR_SEQ (snakemake.logging.ColorizingTextHandler attribute)

ColorizingTextHandler (class in snakemake.logging) colors (snakemake.logging.ColorizingTextHandler attribute) combine_preamble_and_source() (snakemake.script.BashScript method) (snakemake.script.RustScript method) compare() (snakemake.rules.Ruleorder method) Conda (class in snakemake.deployment.conda) conda (snakemake.deployment.conda.Env property) conda_block_conflicting_envvars (snakemake.shell.shell attribute) conda_env (snakemake.rules.Rule property) CondaCleanupMode (class in snakemake.deployment.conda) CondaCleanupPkgs (class in snakemake.settings.enums), [1] CondaEnvDirSpec (class in snakemake.deployment.conda) CondaEnvFileSpec (class in snakemake.deployment.conda) CondaEnvNameSpec (class in snakemake.deployment.conda) CondaEnvSpec (class in snakemake.deployment.conda) CondaEnvSpecType (class in snakemake.deployment.conda) consume() (snakemake.io.QueueInfo method) container_img (snakemake.rules.Rule property) container_img_url (snakemake.deployment.conda.Env property) containerize() (in module snakemake.deployment.containerize) contains_wildcard (snakemake.deployment.conda.CondaEnvDirSpec property) (snakemake.deployment.conda.CondaEnvFileSpec property) (snakemake.deployment.conda.CondaEnvNameSpec property) (snakemake.deployment.conda.CondaEnvSpec property) contains_wildcard() (in module snakemake.io) contains_wildcard_constraints() (in module snakemake.io) content (snakemake.deployment.conda.Env property) content_deploy (snakemake.deployment.conda.Env property) content_hash (snakemake.deployment.conda.Env property) content_pin (snakemake.deployment.conda.Env property) copy_permission_safe() (in module snakemake.common) cores (snakemake.executors.dryrun.Executor property) (snakemake.executors.touch.Executor property) cpu_time (snakemake.benchmark.BenchmarkRecord attribute) cpu_usage (snakemake.benchmark.BenchmarkRecord attribute) create() (snakemake.deployment.conda.Env method) create_archive() (snakemake.deployment.conda.Env method) CreateCondaEnvironmentException CreateRuleException cut_traceback() (in module snakemake.exceptions) cwl() (in module snakemake.cwl) CYAN (snakemake.logging.ColorizingTextHandler attribute) CYCLIC_GRAPH (snakemake.settings.enums.StrictDagEvaluation attribute) CyclicGraphException

D

DaemonTimer (class in snakemake.benchmark) dag_to_cwl() (in module snakemake.cwl) data_collected (snakemake.benchmark.BenchmarkRecord attribute) data_path (snakemake.unit_tests.RuleTest property) deactivate() (snakemake.io.IOCache method) dec_all_methods() (in module snakemake.decorators) decode_arg() (snakemake.resources.DefaultResources class method) decorate() (snakemake.logging.ColorizingTextHandler method) default_dependencies() (snakemake.script.RustScript static method) default_features() (snakemake.script.RustScript static method) DefaultFilter (class in snakemake.logging) DefaultFormatter (class in snakemake.logging)

DefaultResources (class in snakemake.resources) defaults (snakemake.resources.DefaultResources attribute) defaults() (snakemake.resources.ResourceScopes class method) deploy() (snakemake.assets.Assets class method) dict_to_aa() (snakemake.script.BashEncoder static method) dict_to_key_value_args() (in module snakemake.common) DIR (snakemake.deployment.conda.CondaEnvSpecType attribute) directory() (in module snakemake.io) DpathWildcardHandler (class in snakemake.ioutils.lookup) draft() (snakemake.notebook.JupyterNotebook method) draft_and_edit() (snakemake.notebook.JupyterNotebook method) DropboxFileException

E

editable (snakemake.notebook.JupyterNotebook attribute) (snakemake.script.ScriptBase attribute) emit() (snakemake.logging.ColorizingTextHandler method) encode_arg() (snakemake.resources.DefaultResources class 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.BashEncoder class method) (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_snakemake() (snakemake.script.BashEncoder method) encode_value() (snakemake.script.JuliaEncoder class method) (snakemake.script.REncoder class method) ensure() (in module snakemake.io) Env (class in snakemake.deployment.conda) EnvModules (class in snakemake.deployment.env_modules) eval_resource_expression() (in module snakemake.resources) evaluate() (in module snakemake.ioutils.evaluate) (snakemake.script.ScriptBase method) excluded (snakemake.resources.ResourceScopes property) executable() (snakemake.shell.shell class method) execute_deployment_script() (snakemake.deployment.conda.Env method)

execute_script() (snakemake.notebook.JupyterNotebook method) (snakemake.script.BashScript method) (snakemake.script.JuliaScript method) (snakemake.script.PythonScript method) (snakemake.script.RMarkdown method) (snakemake.script.RScript method) (snakemake.script.RustScript method) (snakemake.script.ScriptBase method) (snakemake.script.XonshScript method) Executor (class in snakemake.executors.dryrun) (class in snakemake.executors.touch) exists() (in module snakemake.ioutils.exists) (snakemake.sourcecache.SourceCache method) exists_in_storage (snakemake.io.IOCache property) exists_local (snakemake.io.IOCache property) ExistsDict (class in snakemake.io) expand() (in module snakemake.io) expand_benchmark() (snakemake.rules.Rule method) expand_conda_env() (snakemake.rules.Rule 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) expand_vars_and_user() (in module snakemake.common) expected_path (snakemake.unit_tests.RuleTest property) extract_manifest() (snakemake.script.RustScript static method)

F

FILE (snakemake.deployment.conda.CondaEnvSpecType attribute) filter() (snakemake.logging.DefaultFilter method) find_bash_on_windows() (in module snakemake.utils) find_extension() (in module snakemake.wrapper) finish_sentinel (snakemake.io.QueueInfo attribute) finished (snakemake.io.QueueInfo attribute) first_time (snakemake.benchmark.BenchmarkRecord attribute) flag() (in module snakemake.io) flags (snakemake.io.AnnotatedString property) (snakemake.io.AnnotatedStringInterface property) fmt_regex (snakemake.ioutils.lookup.WildcardHandlerBase attribute) format() (in module snakemake.utils) (snakemake.logging.DefaultFormatter method) format_d3dag() (snakemake.logging.DefaultFormatter method) format_dag_debug() (snakemake.logging.DefaultFormatter method) format_dict() (in module snakemake.logging) format_element() (snakemake.utils.SequenceFormatter method) format_error() (in module snakemake.exceptions) format_exception_to_string() (in module snakemake.exceptions) format_field() (snakemake.utils.AlwaysQuotedFormatter method) (snakemake.utils.QuotedFormatter method) (snakemake.utils.SequenceFormatter method)

format_group_error() (snakemake.logging.DefaultFormatter method) format_group_info() (snakemake.logging.DefaultFormatter method) format_host() (snakemake.logging.DefaultFormatter method) format_info() (snakemake.logging.DefaultFormatter method) format_job_error() (snakemake.logging.DefaultFormatter method) format_job_finished() (snakemake.logging.DefaultFormatter method) format_job_info() (snakemake.logging.DefaultFormatter method) format_percentage() (in module snakemake.logging) format_progress() (snakemake.logging.DefaultFormatter method) format_resource_names() (in module snakemake.logging) format_resources() (in module snakemake.logging) format_run_info() (snakemake.logging.DefaultFormatter method) format_shellcmd() (snakemake.logging.DefaultFormatter method) format_traceback() (in module snakemake.exceptions) format_wildcards() (in module snakemake.logging) from_queue() (in module snakemake.io) from_spec() (snakemake.deployment.conda.CondaEnvSpecType class method) FTPFileException FUNCTIONS (snakemake.settings.enums.StrictDagEvaluation attribute)

G

Gather (class in snakemake.common) generate() (in module snakemake.unit_tests) generate_preamble() (snakemake.script.BashScript static method) (snakemake.script.PythonScript static method) (snakemake.script.RScript static method) (snakemake.script.RustScript static method) GenericSourceFile (class in snakemake.sourcecache) get() (snakemake.checkpoints.Checkpoint method) (snakemake.io.Namedlist method) get_appdirs() (in module snakemake.common) get_basedir() (snakemake.sourcecache.HostingProviderFile method) (snakemake.sourcecache.LocalGitFile method) (snakemake.sourcecache.SourceFile method) get_benchmarks() (snakemake.benchmark.BenchmarkRecord method) get_cache_path() (snakemake.sourcecache.SourceFile method) get_cell_sources() (in module snakemake.notebook) get_conda_env() (in module snakemake.wrapper) (snakemake.deployment.conda.CondaEnvDirSpec method) (snakemake.deployment.conda.CondaEnvFileSpec method) (snakemake.deployment.conda.CondaEnvNameSpec method) (snakemake.deployment.conda.CondaEnvSpec method) get_container_image() (in module snakemake.common) get_content() (snakemake.assets.Asset method) (snakemake.assets.Assets class method) get_env_setup_done_flag_file() (in module snakemake.deployment.conda) get_event_level() (in module snakemake.logging) get_exception_origin() (in module snakemake.exceptions) get_exec_class() (in module snakemake.notebook) get_exec_mode() (snakemake.executors.dryrun.Executor method) (snakemake.executors.touch.Executor method) get_executable() (snakemake.shell.shell class method) get_file_hash() (in module snakemake.common) get_filename() (snakemake.sourcecache.GenericSourceFile method) (snakemake.sourcecache.HostingProviderFile method) (snakemake.sourcecache.LocalGitFile method) (snakemake.sourcecache.LocalSourceFile method) (snakemake.sourcecache.SourceFile method) get_flag_value() (in module snakemake.io) get_function_params() (in module snakemake.common) get_git_root() (in module snakemake.common.git) get_git_root_parent_directory() (in module snakemake.common.git) get_header() (snakemake.benchmark.BenchmarkRecord class method) get_input_function_aux_params() (in module snakemake.common) get_interpreter_exec() (snakemake.notebook.JupyterNotebook method) (snakemake.notebook.PythonJupyterNotebook method) (snakemake.notebook.RJupyterNotebook method) get_language() (in module snakemake.script) get_language_name() (snakemake.notebook.JupyterNotebook method) (snakemake.notebook.PythonJupyterNotebook method) (snakemake.notebook.RJupyterNotebook method)

get_last_stable_version() (in module snakemake.common) get_line() (in module snakemake.linting.snakefiles) get_lineno() (snakemake.linting.rules.RuleLinter method) get_logfile() (snakemake.logging.LoggerManager method) get_name_modifier_func() (in module snakemake.modules) get_path() (in module snakemake.wrapper) (snakemake.sourcecache.SourceCache method) get_path_or_uri() (snakemake.sourcecache.GenericSourceFile method) (snakemake.sourcecache.GithubFile method) (snakemake.sourcecache.GitlabFile method) (snakemake.sourcecache.LocalGitFile method) (snakemake.sourcecache.LocalSourceFile method) (snakemake.sourcecache.SourceFile method) get_preamble() (snakemake.notebook.PythonJupyterNotebook method) (snakemake.notebook.RJupyterNotebook method) (snakemake.script.BashScript method) (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_python_executable() (snakemake.executors.touch.Executor method) get_report_id() (in module snakemake.common) get_rule_whitelist() (snakemake.modules.ModuleInfo method) get_script() (in module snakemake.wrapper) get_singularity_envvars() (snakemake.deployment.conda.Env class method) get_snakefile() (snakemake.modules.ModuleInfo method) get_snakemake_searchpath_mountpoints() (in module snakemake.deployment.singularity) get_snakemake_searchpaths() (in module snakemake.common) get_some_product() (snakemake.rules.Rule method) get_source() (in module snakemake.script) get_uuid() (in module snakemake.common) get_version() (snakemake.assets.Assets class method) get_wildcard_constraints() (in module snakemake.io) get_wildcard_len() (snakemake.rules.Rule static method) get_wildcard_names() (in module snakemake.io) get_wildcards() (snakemake.rules.Rule method) get_wrapper_tag() (snakemake.modules.ModuleInfo method) git_content() (in module snakemake.common.git) GithubFile (class in snakemake.sourcecache) GitlabFile (class in snakemake.sourcecache) glob_wildcards() (in module snakemake.io) globals (snakemake.resources.ResourceScopes property) GREEN (snakemake.logging.ColorizingTextHandler attribute) group (snakemake.rules.Rule property) group_into_chunks() (in module snakemake.common) GroupResources (class in snakemake.resources)

H

handle() (snakemake.ioutils.lookup.WildcardHandlerBase method) handle_job_error() (snakemake.executors.dryrun.Executor method) handle_job_success() (snakemake.executors.dryrun.Executor method) (snakemake.executors.touch.Executor method) has_products() (snakemake.rules.Rule method) has_wildcards() (snakemake.rules.Rule method)

hash (snakemake.deployment.conda.Env property) (snakemake.deployment.env_modules.EnvModules property) (snakemake.deployment.singularity.Image property) HOST (snakemake.settings.enums.Quietness attribute) HostingProviderFile (class in snakemake.sourcecache) htmlindex (snakemake.io.ReportObject attribute) HTTPFileException

I

Image (class in snakemake.deployment.singularity) ImproperOutputException ImproperShadowException IncompleteCheckpointException IncompleteFilesException infer_resources() (in module snakemake.resources) infer_source_file() (in module snakemake.sourcecache) inherit_rule_proxies() (snakemake.modules.WorkflowModifier method) InOutput (class in snakemake.ruleinfo) input (snakemake.benchmark.BenchmarkRecord attribute) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) INPUT (snakemake.settings.enums.ChangeType attribute) (snakemake.settings.enums.RerunTrigger attribute) input_size_mb() (snakemake.benchmark.BenchmarkRecord method) InputFiles (class in snakemake.io) InputFunctionException InputOpenException insert_preamble_cell() (snakemake.notebook.JupyterNotebook method) instance (snakemake.deployment.singularity.Singularity attribute) instance() (snakemake.utils.Paramspace method) instance_patterns (snakemake.utils.Paramspace property) instances (snakemake.deployment.conda.Conda attribute) io_in (snakemake.benchmark.BenchmarkRecord attribute) io_out (snakemake.benchmark.BenchmarkRecord attribute) IOCache (class in snakemake.io) iocache() (in module snakemake.io) IOException IOFile() (in module snakemake.io) IOFileException is_callable() (in module snakemake.io) (snakemake.io.AnnotatedString method) (snakemake.io.AnnotatedStringInterface method) is_containerized (snakemake.deployment.conda.Env property) is_cwl (snakemake.rules.Rule property) is_externally_managed (snakemake.deployment.conda.Env property) is_file (snakemake.deployment.conda.CondaEnvDirSpec property) (snakemake.deployment.conda.CondaEnvFileSpec property) (snakemake.deployment.conda.CondaEnvSpec property) is_file_not_found_error() (in module snakemake.exceptions)

is_flagged() (in module snakemake.io) (snakemake.io.AnnotatedStringInterface method) is_humanfriendly_resource() (in module snakemake.resources) is_initialized (snakemake.deployment.conda.Conda property) is_local (snakemake.deployment.singularity.Image property) (snakemake.sourcecache.GenericSourceFile property) (snakemake.sourcecache.HostingProviderFile property) (snakemake.sourcecache.LocalGitFile property) (snakemake.sourcecache.LocalSourceFile property) (snakemake.sourcecache.SourceFile property) is_local_file() (in module snakemake.common) is_namedtuple_instance() (in module snakemake.common) is_notebook (snakemake.rules.Rule property) is_periodic() (snakemake.io.PeriodicityDetector method) is_persistently_cacheable() (snakemake.sourcecache.GenericSourceFile method) (snakemake.sourcecache.HostingProviderFile method) (snakemake.sourcecache.LocalGitFile method) (snakemake.sourcecache.LocalSourceFile method) (snakemake.sourcecache.SourceFile method) is_producer() (snakemake.rules.Rule method) is_quiet_about() (in module snakemake.logging) is_run (snakemake.rules.Rule property) is_script (snakemake.rules.Rule property) is_script() (in module snakemake.wrapper) is_shell (snakemake.rules.Rule property) is_template_engine (snakemake.rules.Rule property) is_tty (snakemake.logging.ColorizingTextHandler property) is_url() (in module snakemake.wrapper) is_wrapper (snakemake.rules.Rule property) isabs() (snakemake.sourcecache.LocalSourceFile method) ITEM (snakemake.ioutils.rule_items_proxy.KeyKind attribute) item_desc_json() (snakemake.linting.Linter method) (snakemake.linting.rules.RuleLinter method) (snakemake.linting.snakefiles.SnakefileLinter method) item_desc_plain() (snakemake.linting.Linter method) (snakemake.linting.rules.RuleLinter method) (snakemake.linting.snakefiles.SnakefileLinter method) items (snakemake.io.QueueInfo attribute) items() (snakemake.io.Namedlist method) iter_stdout() (snakemake.shell.shell static method)

J

Jinja2Renderer (class in snakemake.template_rendering.jinja2) job_to_cwl() (in module snakemake.cwl) jobid (snakemake.benchmark.BenchmarkRecord attribute) join() (snakemake.sourcecache.HostingProviderFile method) (snakemake.sourcecache.LocalGitFile method) (snakemake.sourcecache.SourceFile method)

JuliaEncoder (class in snakemake.script) JuliaScript (class in snakemake.script) JupyterNotebook (class in snakemake.notebook)

K

KeyKind (class in snakemake.ioutils.rule_items_proxy) keys() (snakemake.io.Namedlist method)

kill() (snakemake.shell.shell class method) kwpaths (snakemake.ruleinfo.InOutput attribute)

L

labels (snakemake.io.ReportObject attribute) last_checked (snakemake.io.QueueInfo attribute) limit() (in module snakemake.io) linecount() (in module snakemake.utils) lineno (snakemake.rules.Rule property) Lint (class in snakemake.linting) lint() (snakemake.linting.Linter method) lint_absolute_paths() (snakemake.linting.snakefiles.SnakefileLinter method) lint_envvars() (snakemake.linting.snakefiles.SnakefileLinter method) lint_iofile_by_index() (snakemake.linting.rules.RuleLinter method) lint_log_directive() (snakemake.linting.rules.RuleLinter method) lint_long_run() (snakemake.linting.rules.RuleLinter method) lint_missing_software_definition() (snakemake.linting.rules.RuleLinter method) lint_mixed_func_and_rules() (snakemake.linting.snakefiles.SnakefileLinter method) lint_not_used_params() (snakemake.linting.rules.RuleLinter method) lint_params_prefix() (snakemake.linting.rules.RuleLinter method) lint_path_add() (snakemake.linting.snakefiles.SnakefileLinter method) lint_singularity() (snakemake.linting.snakefiles.SnakefileLinter method) lint_tab_usage() (snakemake.linting.snakefiles.SnakefileLinter method) Linter (class in snakemake.linting)

lints() (snakemake.linting.Linter method) listfiles() (in module snakemake.utils) load_configfile() (in module snakemake.common.configfile) local() (in module snakemake.io) local_path (snakemake.script.ScriptBase property) LocalGitFile (class in snakemake.sourcecache) locals (snakemake.resources.ResourceScopes property) LocalSourceFile (class in snakemake.sourcecache) lock (snakemake.deployment.conda.Conda attribute) LockException Log (class in snakemake.io) log (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) log_fmt_shell() (snakemake.script.Snakemake method) log_location() (in module snakemake.common) log_verbose_traceback() (in module snakemake.exceptions) logfile_hint() (snakemake.logging.LoggerManager method) LoggerManager (class in snakemake.logging) lookup() (in module snakemake.ioutils.lookup) LookupError lutime() (in module snakemake.io)

M

MAGENTA (snakemake.logging.ColorizingTextHandler attribute) makedirs() (in module snakemake.utils) match() (snakemake.output_index.OutputIndex method) match_producers() (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) mb_to_mib() (in module snakemake.common) mean_load() (snakemake.benchmark.BenchmarkRecord method) messages (snakemake.exceptions.RuleException property) min_version() (in module snakemake.utils) MissingInputException MissingOutputException MissingOutputFileCachePathException MissingRuleException modifier (snakemake.ruleinfo.InOutput attribute) modifies_prefixes (snakemake.path_modifier.PathModifier property) modify() (snakemake.path_modifier.PathModifier method) modify_path() (snakemake.modules.WorkflowModifier method) modify_rulename() (snakemake.modules.WorkflowModifier method) modify_wrapper_uri() (snakemake.modules.WorkflowModifier method) module snakemake snakemake.assets snakemake.benchmark snakemake.checkpoints snakemake.common snakemake.common.argparse snakemake.common.configfile snakemake.common.git snakemake.common.tbdstring snakemake.common.typing snakemake.common.workdir_handler snakemake.cwl snakemake.decorators snakemake.deployment snakemake.deployment.conda snakemake.deployment.containerize snakemake.deployment.env_modules snakemake.deployment.singularity snakemake.exceptions snakemake.executors snakemake.executors.dryrun snakemake.executors.touch snakemake.io snakemake.ioflags snakemake.ioutils snakemake.ioutils.branch snakemake.ioutils.collect snakemake.ioutils.evaluate snakemake.ioutils.exists snakemake.ioutils.lookup snakemake.ioutils.rule_items_proxy snakemake.ioutils.subpath snakemake.linting snakemake.linting.links snakemake.linting.rules snakemake.linting.snakefiles snakemake.logging snakemake.modules snakemake.notebook snakemake.output_index snakemake.path_modifier snakemake.profiles snakemake.remote snakemake.remote.AzBlob snakemake.remote.dropbox snakemake.remote.EGA snakemake.remote.FTP snakemake.remote.gfal snakemake.remote.gridftp snakemake.remote.GS snakemake.remote.HTTP snakemake.remote.iRODS snakemake.remote.NCBI snakemake.remote.S3 snakemake.remote.S3Mocked snakemake.remote.SFTP snakemake.remote.webdav snakemake.remote.XRootD snakemake.remote.zenodo snakemake.resources snakemake.ruleinfo snakemake.rules snakemake.script snakemake.settings, [1] snakemake.settings.enums, [1] snakemake.shell snakemake.sourcecache snakemake.target_jobs snakemake.template_rendering snakemake.template_rendering.jinja2 snakemake.template_rendering.yte snakemake.unit_tests snakemake.unit_tests.templates snakemake.utils snakemake.wrapper

ModuleInfo (class in snakemake.modules) mtime (snakemake.io.IOCache property) MTIME (snakemake.settings.enums.RerunTrigger attribute) mtime() (snakemake.sourcecache.HostingProviderFile method) (snakemake.sourcecache.LocalSourceFile method) (snakemake.sourcecache.SourceFile method) mtime_inventory() (snakemake.io.IOCache method) multiext() (in module snakemake.io)

N

NAME (snakemake.deployment.conda.CondaEnvSpecType attribute) name (snakemake.rules.Rule property) Namedlist (class in snakemake.io) NCBIFileException needs_wildcards() (snakemake.ioutils.lookup.QueryWildcardHandler method) (snakemake.ioutils.lookup.WildcardHandlerBase method)

new_from() (snakemake.io.AnnotatedString method) NoRulesException notebook() (in module snakemake.notebook) num_if_possible() (in module snakemake.common)

O

olddir (snakemake.common.workdir_handler.WorkdirHandler attribute) open() (snakemake.sourcecache.SourceCache method) orig_arg (snakemake.resources.ParsedResource attribute) os_sync() (in module snakemake.utils) output (snakemake.checkpoints.CheckpointJob attribute) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property)

OutputFiles (class in snakemake.io) OutputIndex (class in snakemake.output_index) overwrite_function_params() (in module snakemake.common)

P

Params (class in snakemake.io) params (snakemake.benchmark.BenchmarkRecord attribute) (snakemake.rules.Rule property) (snakemake.rules.RuleProxy property) (snakemake.script.Snakemake property) PARAMS (snakemake.settings.enums.ChangeType attribute) (snakemake.settings.enums.RerunTrigger attribute) Paramspace (class in snakemake.utils) parse() (snakemake.profiles.ProfileConfigFileParser method) parse_key_value_arg() (in module snakemake.common) parse_params() (snakemake.benchmark.BenchmarkRecord method) parse_resources() (in module snakemake.resources) (snakemake.benchmark.BenchmarkRecord method) parse_target_jobs_cli_args() (in module snakemake.target_jobs) parse_uri() (in module snakemake.common) parse_wildcards() (snakemake.benchmark.BenchmarkRecord method) ParsedResource (class in snakemake.resources) parseversion() (snakemake.deployment.singularity.Singularity method) path (snakemake.deployment.singularity.Image property) PathModifier (class in snakemake.path_modifier) paths (snakemake.ruleinfo.InOutput attribute) patterns (snakemake.io.ReportObject attribute) PERIODIC_WILDCARDS (snakemake.settings.enums.StrictDagEvaluation attribute) PeriodicityDetector (class in snakemake.io)

PeriodicWildcardError pid (snakemake.benchmark.BenchmarkTimer attribute) pin_file (snakemake.deployment.conda.Env property) pipe() (in module snakemake.io) post_deploy_file (snakemake.deployment.conda.Env property) prefix() (snakemake.shell.shell class method) pretty_print_iofile() (in module snakemake.io) prev_time (snakemake.benchmark.BenchmarkRecord attribute) print_benchmark_jsonl() (in module snakemake.benchmark) print_benchmark_tsv() (in module snakemake.benchmark) print_exception() (in module snakemake.exceptions) print_exception_warning() (in module snakemake.exceptions) printcache() (snakemake.executors.dryrun.Executor method) printjob() (snakemake.executors.dryrun.Executor method) processed_procs (snakemake.benchmark.BenchmarkRecord attribute) procs (snakemake.benchmark.BenchmarkTimer attribute) products() (snakemake.rules.Rule method) ProfileConfigFileParser (class in snakemake.profiles) PROGRESS (snakemake.settings.enums.Quietness attribute) protected() (in module snakemake.io) ProtectedOutputException pull() (snakemake.deployment.singularity.Image method) PythonJupyterNotebook (class in snakemake.notebook) PythonScript (class in snakemake.script)

Q

QueryWildcardHandler (class in snakemake.ioutils.lookup) queue (snakemake.io.QueueInfo attribute)

QueueInfo (class in snakemake.io) Quietness (class in snakemake.settings.enums), [1] QuotedFormatter (class in snakemake.utils)

R

R() (in module snakemake.utils) read_item() (snakemake.linting.Linter method) (snakemake.linting.snakefiles.SnakefileLinter method) read_job_properties() (in module snakemake.utils) REASON (snakemake.settings.enums.Quietness attribute) RED (snakemake.logging.ColorizingTextHandler attribute) ref (snakemake.sourcecache.HostingProviderFile property) (snakemake.sourcecache.LocalGitFile property) ref_attributes (snakemake.ruleinfo.RuleInfo attribute) regex_from_filepattern() (in module snakemake.io) register() (snakemake.checkpoints.Checkpoints method) register_in_globals() (in module snakemake.ioflags) (in module snakemake.ioutils) register_parser_action() (in module snakemake.common.argparse) register_wildcards() (snakemake.rules.Rule method) RemoteFileException RemoteProvider (class in snakemake.remote.AzBlob) (class in snakemake.remote.dropbox) (class in snakemake.remote.EGA) (class in snakemake.remote.FTP) (class in snakemake.remote.gfal) (class in snakemake.remote.gridftp) (class in snakemake.remote.GS) (class in snakemake.remote.HTTP) (class in snakemake.remote.iRODS) (class in snakemake.remote.NCBI) (class in snakemake.remote.S3) (class in snakemake.remote.S3Mocked) (class in snakemake.remote.SFTP) (class in snakemake.remote.webdav) (class in snakemake.remote.XRootD) (class in snakemake.remote.zenodo) RemoteProviderBase (class in snakemake.remote) remove() (in module snakemake.io) remove_preamble_cell() (snakemake.notebook.JupyterNotebook method) REncoder (class in snakemake.script) render() (snakemake.template_rendering.jinja2.Jinja2Renderer method) (snakemake.template_rendering.TemplateRenderer method) (snakemake.template_rendering.yte.YteRenderer method)

render_template() (in module snakemake.template_rendering) repeat() (in module snakemake.io) replace_prefix() (snakemake.path_modifier.PathModifier method) report() (in module snakemake.io) (in module snakemake.utils) report_href() (snakemake.script.Snakemake method) ReportHref (class in snakemake.script) ReportObject (class in snakemake.io) RerunTrigger (class in snakemake.settings.enums), [1] RESET_SEQ (snakemake.logging.ColorizingTextHandler attribute) Resources (class in snakemake.io) resources (snakemake.benchmark.BenchmarkRecord attribute) ResourceScopes (class in snakemake.resources) ResourceScopesException restart_times (snakemake.rules.Rule property) RJupyterNotebook (class in snakemake.notebook) RMarkdown (class in snakemake.script) RScript (class in snakemake.script) Rule (class in snakemake.rules) rule (snakemake.checkpoints.Checkpoint attribute) (snakemake.checkpoints.CheckpointJob attribute) rule_item_factory() (in module snakemake.ioutils.rule_items_proxy) rule_name (snakemake.benchmark.BenchmarkRecord attribute) RuleException RuleInfo (class in snakemake.ruleinfo) RuleItemProxy (class in snakemake.ioutils.rule_items_proxy) RuleLinter (class in snakemake.linting.rules) Ruleorder (class in snakemake.rules) RuleProxy (class in snakemake.rules) Rules (class in snakemake.common) RULES (snakemake.settings.enums.Quietness attribute) RuleTest (class in snakemake.unit_tests) run() (snakemake.benchmark.DaemonTimer method) run_job() (snakemake.executors.dryrun.Executor method) (snakemake.executors.touch.Executor method) running_time (snakemake.benchmark.BenchmarkRecord attribute) runtime_cache_path (snakemake.sourcecache.SourceCache property) RustScript (class in snakemake.script)

S

S3FileException Scatter (class in snakemake.common) ScheduledPeriodicTimer (class in snakemake.benchmark) script() (in module snakemake.script) ScriptBase (class in snakemake.script) SequenceFormatter (class in snakemake.utils) service() (in module snakemake.io) set_env() (in module snakemake.common) set_input() (snakemake.rules.Rule method) set_log() (snakemake.rules.Rule method) set_output() (snakemake.rules.Rule method) set_params() (snakemake.rules.Rule method) set_resource() (snakemake.resources.DefaultResources method) set_wildcard_constraints() (snakemake.rules.Rule method) setup() (snakemake.logging.LoggerManager method) setup_logfile() (snakemake.logging.LoggerManager method) SFTPFileException sha256 (snakemake.assets.Asset attribute) shell (class in snakemake.shell) shellcmd() (in module snakemake.deployment.singularity) (snakemake.deployment.conda.Conda method) (snakemake.deployment.env_modules.EnvModules method) shellcmd_win() (snakemake.deployment.conda.Conda method) show_logs() (in module snakemake.logging) shutdown() (snakemake.executors.dryrun.Executor method) (snakemake.executors.touch.Executor method) simplify_path() (in module snakemake.utils) (snakemake.sourcecache.LocalSourceFile method) (snakemake.sourcecache.SourceFile method) Singularity (class in snakemake.deployment.singularity) size (snakemake.io.InputFiles property) (snakemake.io.IOCache property) size_files (snakemake.io.InputFiles property) size_files_gb (snakemake.io.InputFiles property) size_files_kb (snakemake.io.InputFiles property) size_files_mb (snakemake.io.InputFiles property) size_gb (snakemake.io.InputFiles property) size_kb (snakemake.io.InputFiles property) size_mb (snakemake.io.InputFiles property) skip_rule() (snakemake.modules.WorkflowModifier method) skipped_procs (snakemake.benchmark.BenchmarkRecord attribute) smart_join() (in module snakemake.common) snakefile (snakemake.rules.Rule property) SnakefileLinter (class in snakemake.linting.snakefiles) snakemake module Snakemake (class in snakemake.script) snakemake (in module snakemake.script) snakemake.assets module snakemake.benchmark module snakemake.checkpoints module snakemake.common module snakemake.common.argparse module snakemake.common.configfile module snakemake.common.git module snakemake.common.tbdstring module snakemake.common.typing module snakemake.common.workdir_handler module snakemake.cwl module snakemake.decorators module snakemake.deployment module snakemake.deployment.conda module snakemake.deployment.containerize module snakemake.deployment.env_modules module snakemake.deployment.singularity module snakemake.exceptions module snakemake.executors module snakemake.executors.dryrun module snakemake.executors.touch module snakemake.io module snakemake.ioflags module snakemake.ioutils module snakemake.ioutils.branch module snakemake.ioutils.collect module snakemake.ioutils.evaluate module snakemake.ioutils.exists module snakemake.ioutils.lookup module

snakemake.ioutils.rule_items_proxy module snakemake.ioutils.subpath module snakemake.linting module snakemake.linting.links module snakemake.linting.rules module snakemake.linting.snakefiles module snakemake.logging module snakemake.modules module snakemake.notebook module snakemake.output_index module snakemake.path_modifier module snakemake.profiles module snakemake.remote module snakemake.remote.AzBlob module snakemake.remote.dropbox module snakemake.remote.EGA module snakemake.remote.FTP module snakemake.remote.gfal module snakemake.remote.gridftp module snakemake.remote.GS module snakemake.remote.HTTP module snakemake.remote.iRODS module snakemake.remote.NCBI module snakemake.remote.S3 module snakemake.remote.S3Mocked module snakemake.remote.SFTP module snakemake.remote.webdav module snakemake.remote.XRootD module snakemake.remote.zenodo module snakemake.resources module snakemake.ruleinfo module snakemake.rules module snakemake.script module snakemake.settings module, [1] snakemake.settings.enums module, [1] snakemake.shell module snakemake.sourcecache module snakemake.target_jobs module snakemake.template_rendering module snakemake.template_rendering.jinja2 module snakemake.template_rendering.yte module snakemake.unit_tests module snakemake.unit_tests.templates module snakemake.utils module snakemake.wrapper module SOFTWARE_ENV (snakemake.settings.enums.RerunTrigger attribute) SourceCache (class in snakemake.sourcecache) sourcecache_entry() (in module snakemake.io) SourceFile (class in snakemake.sourcecache) SourceFileError SpawnedJobError spec (snakemake.assets.Assets attribute) split_git_path() (in module snakemake.common.git) start() (snakemake.benchmark.ScheduledPeriodicTimer method) stop() (snakemake.logging.LoggerManager method) StrictDagEvaluation (class in snakemake.settings.enums), [1] strip_prefix() (in module snakemake.common) strip_re() (in module snakemake.script) strip_wildcard_constraints() (in module snakemake.io) subcategory (snakemake.io.ReportObject attribute) subpath() (in module snakemake.ioutils.subpath) suffix() (snakemake.shell.shell class method)

T

tarballs (snakemake.deployment.conda.CondaCleanupMode attribute) TARBALLS (snakemake.settings.enums.CondaCleanupPkgs attribute) target (snakemake.unit_tests.RuleTest property) TBDString (class in snakemake.common.tbdstring) temp() (in module snakemake.io) TemplateRenderer (class in snakemake.template_rendering) temporary() (in module snakemake.io)

terminate() (snakemake.shell.shell class method) TerminatedException threads (snakemake.benchmark.BenchmarkRecord attribute) timedelta_to_str() (snakemake.benchmark.BenchmarkRecord method) timestamp() (in module snakemake.logging) to_json() (snakemake.benchmark.BenchmarkRecord method) to_tsv() (snakemake.benchmark.BenchmarkRecord method) touch() (in module snakemake.io)

U

Unformattable (class in snakemake.utils) unique_justseen() (in module snakemake.common) UnknownRuleException unpack() (in module snakemake.io) update() (in module snakemake.ioflags) (snakemake.io.Namedlist method) update_config() (in module snakemake.utils)

update_last_checked() (snakemake.io.QueueInfo method) update_lineno() (in module snakemake.exceptions) update_wildcard_constraints() (in module snakemake.io) (snakemake.rules.Rule method) url (snakemake.assets.Asset attribute) url_args() (snakemake.script.ReportHref method) use_rules() (snakemake.modules.ModuleInfo method)

V

valid_repo (snakemake.sourcecache.HostingProviderFile attribute) validate() (in module snakemake.utils) value (snakemake.resources.ParsedResource attribute)

variables (snakemake.template_rendering.TemplateRenderer property) version (snakemake.assets.Asset attribute) (snakemake.deployment.singularity.Singularity property)

W

wait_for_files() (in module snakemake.io) WebDAVFileException WHITE (snakemake.logging.ColorizingTextHandler attribute) wildcard_constraints (snakemake.rules.Rule property) wildcard_names (snakemake.rules.Rule property) wildcard_pattern (snakemake.utils.Paramspace property) WildcardError WildcardHandlerBase (class in snakemake.ioutils.lookup) Wildcards (class in snakemake.io) wildcards (snakemake.benchmark.BenchmarkRecord attribute) win_command_prefix() (snakemake.shell.shell class method) work() (snakemake.benchmark.BenchmarkTimer method) (snakemake.benchmark.ScheduledPeriodicTimer method)

workdir (snakemake.common.workdir_handler.WorkdirHandler attribute) WorkdirHandler (class in snakemake.common.workdir_handler) WorkflowModifier (class in snakemake.modules) wrapper() (in module snakemake.wrapper) write_benchmark_records() (in module snakemake.benchmark) write_script() (snakemake.notebook.JupyterNotebook method) (snakemake.script.BashScript method) (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

XonshScript (class in snakemake.script)

XRootDFileException

Y

YELLOW (snakemake.logging.ColorizingTextHandler attribute)

yellow_info_events (snakemake.logging.ColorizingTextHandler attribute) YteRenderer (class in snakemake.template_rendering.yte)

Z

ZenodoFileException