snakemake

• snakemake package
  • Subpackages
    • snakemake.assets package
      • Module contents
    • snakemake.caching package
      • Submodules
      • snakemake.caching.hash module
      • snakemake.caching.local module
      • snakemake.caching.storage module
      • Module contents
    • snakemake.common package
      • Subpackages
      • Submodules
      • 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
      • Module contents
    • snakemake.deployment package
      • Submodules
      • snakemake.deployment.conda module
      • snakemake.deployment.containerize module
      • snakemake.deployment.env_modules module
      • snakemake.deployment.singularity module
      • Module contents
    • snakemake.executors package
      • Submodules
      • snakemake.executors.dryrun module
      • snakemake.executors.local module
      • snakemake.executors.touch module
      • Module contents
    • snakemake.ioutils package
      • Submodules
      • 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
      • Module contents
    • snakemake.linting package
      • Submodules
      • snakemake.linting.links module
      • snakemake.linting.rules module
      • snakemake.linting.snakefiles module
      • Module contents
    • snakemake.remote package
      • Submodules
      • snakemake.remote.AzBlob module
      • snakemake.remote.EGA module
      • snakemake.remote.FTP module
      • snakemake.remote.GS module
      • snakemake.remote.HTTP module
      • snakemake.remote.NCBI module
      • snakemake.remote.S3 module
      • snakemake.remote.S3Mocked module
      • snakemake.remote.SFTP module
      • snakemake.remote.XRootD module
      • snakemake.remote.dropbox module
      • snakemake.remote.gfal module
      • snakemake.remote.gridftp module
      • snakemake.remote.iRODS module
      • snakemake.remote.webdav module
      • snakemake.remote.zenodo module
      • Module contents
    • snakemake.report package
      • Subpackages
      • Submodules
      • snakemake.report.common module
      • snakemake.report.rulegraph_spec module
      • Module contents
    • snakemake.script package
      • Module contents
    • snakemake.settings package
      • Submodules
      • snakemake.settings.enums module
      • snakemake.settings.types module
      • Module contents
    • snakemake.template_rendering package
      • Submodules
      • snakemake.template_rendering.jinja2 module
      • snakemake.template_rendering.yte module
      • Module contents
    • snakemake.unit_tests package
      • Subpackages
      • Module contents
  • Submodules
  • snakemake.api module
  • snakemake.benchmark module
    • BENCHMARK_INTERVAL
    • BENCHMARK_INTERVAL_SHORT
    • BenchmarkRecord
      • BenchmarkRecord.cpu_time
      • BenchmarkRecord.cpu_usage
      • BenchmarkRecord.data_collected
      • BenchmarkRecord.first_time
      • BenchmarkRecord.get_benchmarks()
      • BenchmarkRecord.get_header()
      • BenchmarkRecord.input
      • BenchmarkRecord.input_size_mb()
      • BenchmarkRecord.io_in
      • BenchmarkRecord.io_out
      • BenchmarkRecord.jobid
      • BenchmarkRecord.max_pss
      • BenchmarkRecord.max_rss
      • BenchmarkRecord.max_uss
      • BenchmarkRecord.max_vms
      • BenchmarkRecord.mean_load()
      • BenchmarkRecord.params
      • BenchmarkRecord.parse_params()
      • BenchmarkRecord.parse_resources()
      • BenchmarkRecord.parse_wildcards()
      • BenchmarkRecord.prev_time
      • BenchmarkRecord.processed_procs
      • BenchmarkRecord.resources
      • BenchmarkRecord.rule_name
      • BenchmarkRecord.running_time
      • BenchmarkRecord.skipped_procs
      • BenchmarkRecord.threads
      • BenchmarkRecord.timedelta_to_str()
      • BenchmarkRecord.to_json()
      • BenchmarkRecord.to_tsv()
      • BenchmarkRecord.wildcards
    • BenchmarkTimer
      • BenchmarkTimer.bench_record
      • BenchmarkTimer.pid
      • BenchmarkTimer.procs
      • BenchmarkTimer.work()
    • DaemonTimer
      • DaemonTimer.cancel()
      • DaemonTimer.run()
    • ScheduledPeriodicTimer
      • ScheduledPeriodicTimer.cancel()
      • ScheduledPeriodicTimer.start()
      • ScheduledPeriodicTimer.work()
    • benchmarked()
    • print_benchmark_jsonl()
    • print_benchmark_tsv()
    • write_benchmark_records()
  • snakemake.checkpoints module
    • Checkpoint
      • Checkpoint.checkpoints
      • Checkpoint.get()
      • Checkpoint.rule
    • CheckpointJob
      • CheckpointJob.output
      • CheckpointJob.rule
    • Checkpoints
      • Checkpoints.register()
  • snakemake.cli module
  • snakemake.cwl module
    • cwl()
    • dag_to_cwl()
    • job_to_cwl()
  • snakemake.dag module
  • snakemake.decorators module
    • dec_all_methods()
  • snakemake.exceptions module
    • AmbiguousRuleException
    • AzureFileException
    • CacheMissException
    • CheckSumMismatchException
    • ChildIOException
    • CliException
    • ClusterJobException
    • CreateCondaEnvironmentException
    • CreateRuleException
    • CyclicGraphException
    • DropboxFileException
    • FTPFileException
    • HTTPFileException
    • IOException
    • IOFileException
    • ImproperOutputException
    • ImproperShadowException
    • IncompleteCheckpointException
    • IncompleteFilesException
    • InputFunctionException
    • InputOpenException
    • LockException
    • LookupError
    • MissingInputException
    • MissingOutputException
    • MissingOutputFileCachePathException
    • MissingRuleException
    • NCBIFileException
    • NoRulesException
    • PeriodicWildcardError
    • ProtectedOutputException
    • RemoteFileException
    • ResourceScopesException
    • RuleException
      • RuleException.messages
    • S3FileException
    • SFTPFileException
    • SourceFileError
    • SpawnedJobError
    • TerminatedException
    • UnknownRuleException
    • WebDAVFileException
    • WildcardError
    • XRootDFileException
    • ZenodoFileException
    • cut_traceback()
    • format_error()
    • format_exception_to_string()
    • format_traceback()
    • get_exception_origin()
    • is_file_not_found_error()
    • log_verbose_traceback()
    • print_exception()
    • print_exception_warning()
    • update_lineno()
  • snakemake.gui module
  • snakemake.io module
    • AnnotatedString
      • AnnotatedString.flags
      • AnnotatedString.is_callable()
      • AnnotatedString.new_from()
    • AnnotatedStringInterface
      • AnnotatedStringInterface.flags
      • AnnotatedStringInterface.is_callable()
      • AnnotatedStringInterface.is_flagged()
    • AttributeGuard
    • ExistsDict
    • IOCache
      • IOCache.clear()
      • IOCache.collect_mtime()
      • IOCache.deactivate()
      • IOCache.exists_in_storage
      • IOCache.exists_local
      • IOCache.mtime
      • IOCache.mtime_inventory()
      • IOCache.size
    • IOFile()
    • InputFiles
      • InputFiles.size
      • InputFiles.size_files
      • InputFiles.size_files_gb
      • InputFiles.size_files_kb
      • InputFiles.size_files_mb
      • InputFiles.size_gb
      • InputFiles.size_kb
      • InputFiles.size_mb
    • Log
    • Namedlist
      • Namedlist.get()
      • Namedlist.items()
      • Namedlist.keys()
      • Namedlist.update()
    • OutputFiles
    • Params
    • PeriodicityDetector
      • PeriodicityDetector.is_periodic()
    • QueueInfo
      • QueueInfo.consume()
      • QueueInfo.finish_sentinel
      • QueueInfo.finished
      • QueueInfo.items
      • QueueInfo.last_checked
      • QueueInfo.queue
      • QueueInfo.update_last_checked()
    • ReportObject
      • ReportObject.caption
      • ReportObject.category
      • ReportObject.htmlindex
      • ReportObject.labels
      • ReportObject.patterns
      • ReportObject.subcategory
    • Resources
    • Wildcards
    • ancient()
    • apply_wildcards()
    • checkpoint_target()
    • contains_wildcard()
    • contains_wildcard_constraints()
    • directory()
    • ensure()
    • expand()
    • flag()
    • from_queue()
    • get_flag_value()
    • get_wildcard_constraints()
    • get_wildcard_names()
    • glob_wildcards()
    • iocache()
    • is_callable()
    • is_flagged()
    • limit()
    • local()
    • lutime()
    • multiext()
    • pipe()
    • pretty_print_iofile()
    • protected()
    • regex_from_filepattern()
    • remove()
    • repeat()
    • report()
    • service()
    • sourcecache_entry()
    • strip_wildcard_constraints()
    • temp()
    • temporary()
    • touch()
    • unpack()
    • update_wildcard_constraints()
    • wait_for_files()
  • snakemake.ioflags module
    • before_update()
    • register_in_globals()
    • update()
  • snakemake.jobs module
  • snakemake.logging module
    • ColorizingTextHandler
      • ColorizingTextHandler.BLACK
      • ColorizingTextHandler.BLUE
      • ColorizingTextHandler.BOLD_SEQ
      • ColorizingTextHandler.COLOR_SEQ
      • ColorizingTextHandler.CYAN
      • ColorizingTextHandler.GREEN
      • ColorizingTextHandler.MAGENTA
      • ColorizingTextHandler.RED
      • ColorizingTextHandler.RESET_SEQ
      • ColorizingTextHandler.WHITE
      • ColorizingTextHandler.YELLOW
      • ColorizingTextHandler.can_color_tty()
      • ColorizingTextHandler.colors
      • ColorizingTextHandler.decorate()
      • ColorizingTextHandler.emit()
      • ColorizingTextHandler.is_tty
      • ColorizingTextHandler.yellow_info_events
    • DefaultFilter
      • DefaultFilter.filter()
    • DefaultFormatter
      • DefaultFormatter.format()
      • DefaultFormatter.format_d3dag()
      • DefaultFormatter.format_dag_debug()
      • DefaultFormatter.format_group_error()
      • DefaultFormatter.format_group_info()
      • DefaultFormatter.format_host()
      • DefaultFormatter.format_info()
      • DefaultFormatter.format_job_error()
      • DefaultFormatter.format_job_finished()
      • DefaultFormatter.format_job_info()
      • DefaultFormatter.format_progress()
      • DefaultFormatter.format_run_info()
      • DefaultFormatter.format_shellcmd()
    • LoggerManager
      • LoggerManager.cleanup_logfile()
      • LoggerManager.get_logfile()
      • LoggerManager.logfile_hint()
      • LoggerManager.setup()
      • LoggerManager.setup_logfile()
      • LoggerManager.stop()
    • format_dict()
    • format_percentage()
    • format_resource_names()
    • format_resources()
    • format_wildcards()
    • get_event_level()
    • is_quiet_about()
    • show_logs()
    • timestamp()
  • snakemake.modules module
    • ModuleInfo
      • ModuleInfo.get_rule_whitelist()
      • ModuleInfo.get_snakefile()
      • ModuleInfo.get_wrapper_tag()
      • ModuleInfo.use_rules()
    • WorkflowModifier
      • WorkflowModifier.inherit_rule_proxies()
      • WorkflowModifier.modify_path()
      • WorkflowModifier.modify_rulename()
      • WorkflowModifier.modify_wrapper_uri()
      • WorkflowModifier.skip_rule()
    • get_name_modifier_func()
  • snakemake.notebook module
    • JupyterNotebook
      • JupyterNotebook.draft()
      • JupyterNotebook.draft_and_edit()
      • JupyterNotebook.editable
      • JupyterNotebook.execute_script()
      • JupyterNotebook.get_interpreter_exec()
      • JupyterNotebook.get_language_name()
      • JupyterNotebook.insert_preamble_cell()
      • JupyterNotebook.remove_preamble_cell()
      • JupyterNotebook.write_script()
    • PythonJupyterNotebook
      • PythonJupyterNotebook.get_interpreter_exec()
      • PythonJupyterNotebook.get_language_name()
      • PythonJupyterNotebook.get_preamble()
    • RJupyterNotebook
      • RJupyterNotebook.get_interpreter_exec()
      • RJupyterNotebook.get_language_name()
      • RJupyterNotebook.get_preamble()
    • get_cell_sources()
    • get_exec_class()
    • notebook()
  • snakemake.output_index module
    • OutputIndex
      • OutputIndex.match()
      • OutputIndex.match_producers()
  • snakemake.parser module
  • snakemake.path_modifier module
    • PathModifier
      • PathModifier.apply_default_storage()
      • PathModifier.modifies_prefixes
      • PathModifier.modify()
      • PathModifier.replace_prefix()
  • snakemake.persistence module
  • snakemake.profiles module
    • ProfileConfigFileParser
      • ProfileConfigFileParser.parse()
  • snakemake.resources module
    • DefaultResources
      • DefaultResources.args
      • DefaultResources.bare_defaults
      • DefaultResources.decode_arg()
      • DefaultResources.defaults
      • DefaultResources.encode_arg()
      • DefaultResources.set_resource()
    • GroupResources
      • GroupResources.basic_layered()
    • ParsedResource
      • ParsedResource.orig_arg
      • ParsedResource.value
    • ResourceScopes
      • ResourceScopes.defaults()
      • ResourceScopes.excluded
      • ResourceScopes.globals
      • ResourceScopes.locals
    • eval_resource_expression()
    • infer_resources()
    • is_humanfriendly_resource()
    • parse_resources()
  • snakemake.ruleinfo module
    • InOutput
      • InOutput.kwpaths
      • InOutput.modifier
      • InOutput.paths
    • RuleInfo
      • RuleInfo.apply_modifier()
      • RuleInfo.ref_attributes
  • snakemake.rules module
    • Rule
      • Rule.apply_input_function()
      • Rule.apply_path_modifier()
      • Rule.benchmark
      • Rule.check_caching()
      • Rule.check_output_duplicates()
      • Rule.check_wildcards()
      • Rule.conda_env
      • Rule.container_img
      • Rule.expand_benchmark()
      • Rule.expand_conda_env()
      • Rule.expand_group()
      • Rule.expand_input()
      • Rule.expand_log()
      • Rule.expand_output()
      • Rule.expand_params()
      • Rule.expand_resources()
      • Rule.get_some_product()
      • Rule.get_wildcard_len()
      • Rule.get_wildcards()
      • Rule.group
      • Rule.has_products()
      • Rule.has_wildcards()
      • Rule.input
      • Rule.is_cwl
      • Rule.is_notebook
      • Rule.is_producer()
      • Rule.is_run
      • Rule.is_script
      • Rule.is_shell
      • Rule.is_template_engine
      • Rule.is_wrapper
      • Rule.lineno
      • Rule.log
      • Rule.name
      • Rule.output
      • Rule.params
      • Rule.products()
      • Rule.register_wildcards()
      • Rule.restart_times
      • Rule.set_input()
      • Rule.set_log()
      • Rule.set_output()
      • Rule.set_params()
      • Rule.set_wildcard_constraints()
      • Rule.snakefile
      • Rule.update_wildcard_constraints()
      • Rule.wildcard_constraints
      • Rule.wildcard_names
    • RuleProxy
      • RuleProxy.benchmark
      • RuleProxy.input
      • RuleProxy.log
      • RuleProxy.output
      • RuleProxy.params
    • Ruleorder
      • Ruleorder.add()
      • Ruleorder.compare()
  • snakemake.scheduler module
  • snakemake.shell module
    • shell
      • shell.check_output()
      • shell.cleanup()
      • shell.conda_block_conflicting_envvars
      • shell.executable()
      • shell.get_executable()
      • shell.iter_stdout()
      • shell.kill()
      • shell.prefix()
      • shell.suffix()
      • shell.terminate()
      • shell.win_command_prefix()
  • snakemake.sourcecache module
    • GenericSourceFile
      • GenericSourceFile.get_filename()
      • GenericSourceFile.get_path_or_uri()
      • GenericSourceFile.is_local
      • GenericSourceFile.is_persistently_cacheable()
    • GithubFile
      • GithubFile.get_path_or_uri()
    • GitlabFile
      • GitlabFile.get_path_or_uri()
    • HostingProviderFile
      • HostingProviderFile.get_basedir()
      • HostingProviderFile.get_filename()
      • HostingProviderFile.is_local
      • HostingProviderFile.is_persistently_cacheable()
      • HostingProviderFile.join()
      • HostingProviderFile.mtime()
      • HostingProviderFile.ref
      • HostingProviderFile.valid_repo
    • LocalGitFile
      • LocalGitFile.get_basedir()
      • LocalGitFile.get_filename()
      • LocalGitFile.get_path_or_uri()
      • LocalGitFile.is_local
      • LocalGitFile.is_persistently_cacheable()
      • LocalGitFile.join()
      • LocalGitFile.ref
    • LocalSourceFile
      • LocalSourceFile.abspath()
      • LocalSourceFile.get_filename()
      • LocalSourceFile.get_path_or_uri()
      • LocalSourceFile.is_local
      • LocalSourceFile.is_persistently_cacheable()
      • LocalSourceFile.isabs()
      • LocalSourceFile.mtime()
      • LocalSourceFile.simplify_path()
    • SourceCache
      • SourceCache.cache_whitelist
      • SourceCache.exists()
      • SourceCache.get_path()
      • SourceCache.open()
      • SourceCache.runtime_cache_path
    • SourceFile
      • SourceFile.get_basedir()
      • SourceFile.get_cache_path()
      • SourceFile.get_filename()
      • SourceFile.get_path_or_uri()
      • SourceFile.is_local
      • SourceFile.is_persistently_cacheable()
      • SourceFile.join()
      • SourceFile.mtime()
      • SourceFile.simplify_path()
    • infer_source_file()
  • snakemake.spawn_jobs module
  • snakemake.storage module
  • snakemake.target_jobs module
    • parse_target_jobs_cli_args()
  • snakemake.utils module
    • AlwaysQuotedFormatter
      • AlwaysQuotedFormatter.format_field()
    • Paramspace
      • Paramspace.instance()
      • Paramspace.instance_patterns
      • Paramspace.wildcard_pattern
    • QuotedFormatter
      • QuotedFormatter.format_field()
    • R()
    • SequenceFormatter
      • SequenceFormatter.format_element()
      • SequenceFormatter.format_field()
    • Unformattable
    • argvquote()
    • available_cpu_count()
    • cmd_exe_quote()
    • find_bash_on_windows()
    • format()
    • linecount()
    • listfiles()
    • makedirs()
    • min_version()
    • os_sync()
    • read_job_properties()
    • report()
    • simplify_path()
    • update_config()
    • validate()
  • snakemake.workflow module
  • snakemake.wrapper module
    • find_extension()
    • get_conda_env()
    • get_path()
    • get_script()
    • is_script()
    • is_url()
    • wrapper()
  • Module contents