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Index
Index
_
__init__() (snakemake.benchmark.BenchmarkRecord method)
(snakemake.benchmark.BenchmarkTimer method)
(snakemake.benchmark.DaemonTimer method)
(snakemake.benchmark.ScheduledPeriodicTimer method)
(snakemake.checkpoints.Checkpoint method)
(snakemake.checkpoints.CheckpointJob method)
(snakemake.checkpoints.Checkpoints method)
(snakemake.common.argparse.ArgumentGroup method)
(snakemake.common.argparse.ArgumentParser method)
(snakemake.common.Gather method)
(snakemake.common.Rules method)
(snakemake.common.Scatter method)
(snakemake.common.tbdstring.TBDString method)
(snakemake.common.workdir_handler.WorkdirHandler method)
(snakemake.deployment.conda.Conda method)
(snakemake.deployment.conda.CondaCleanupMode method)
(snakemake.deployment.conda.CondaEnvFileSpec method)
(snakemake.deployment.conda.CondaEnvNameSpec method)
(snakemake.deployment.conda.CondaEnvSpec method)
(snakemake.deployment.conda.Env method)
(snakemake.deployment.env_modules.EnvModules method)
(snakemake.deployment.singularity.Image method)
(snakemake.deployment.singularity.Singularity method)
(snakemake.executors.dryrun.Executor method)
(snakemake.executors.touch.Executor method)
(snakemake.io.AnnotatedString method)
(snakemake.io.AnnotatedStringInterface method)
(snakemake.io.ExistsDict method)
(snakemake.io.InputFiles method)
(snakemake.io.IOCache method)
(snakemake.io.Log method)
(snakemake.io.Namedlist method)
(snakemake.io.OutputFiles method)
(snakemake.io.Params method)
(snakemake.io.PeriodicityDetector method)
(snakemake.io.QueueInfo method)
(snakemake.io.ReportObject method)
(snakemake.io.Resources method)
(snakemake.io.Wildcards method)
(snakemake.linting.Lint method)
(snakemake.linting.Linter method)
(snakemake.linting.rules.RuleLinter method)
(snakemake.linting.snakefiles.SnakefileLinter method)
(snakemake.logging.ColorizingStreamHandler method)
(snakemake.logging.Logger method)
(snakemake.logging.SlackLogger method)
(snakemake.logging.WMSLogger method)
(snakemake.modules.ModuleInfo method)
(snakemake.modules.WorkflowModifier method)
(snakemake.notebook.JupyterNotebook method)
(snakemake.notebook.PythonJupyterNotebook method)
(snakemake.notebook.RJupyterNotebook method)
(snakemake.output_index.OutputIndex method)
(snakemake.path_modifier.PathModifier method)
(snakemake.profiles.ProfileConfigFileParser method)
(snakemake.resources.DefaultResources method)
(snakemake.resources.GroupResources method)
(snakemake.resources.ParsedResource method)
(snakemake.resources.ResourceScopes method)
(snakemake.ruleinfo.InOutput method)
(snakemake.ruleinfo.RuleInfo method)
(snakemake.rules.Rule method)
(snakemake.rules.Ruleorder method)
(snakemake.rules.RuleProxy method)
(snakemake.scheduler.DummyRateLimiter method)
(snakemake.scheduler.JobScheduler method)
(snakemake.script.BashEncoder method)
(snakemake.script.BashScript method)
(snakemake.script.JuliaEncoder method)
(snakemake.script.JuliaScript method)
(snakemake.script.PythonScript method)
(snakemake.script.REncoder method)
(snakemake.script.RMarkdown method)
(snakemake.script.RScript method)
(snakemake.script.RustScript method)
(snakemake.script.ScriptBase method)
(snakemake.script.Snakemake method)
(snakemake.sourcecache.GenericSourceFile method)
(snakemake.sourcecache.GithubFile method)
(snakemake.sourcecache.GitlabFile method)
(snakemake.sourcecache.HostingProviderFile method)
(snakemake.sourcecache.LocalGitFile method)
(snakemake.sourcecache.LocalSourceFile method)
(snakemake.sourcecache.SourceCache method)
(snakemake.sourcecache.SourceFile method)
(snakemake.template_rendering.jinja2.Jinja2Renderer method)
(snakemake.template_rendering.TemplateRenderer method)
(snakemake.template_rendering.yte.YteRenderer method)
(snakemake.unit_tests.RuleTest method)
A
AlwaysQuotedFormatter (class in snakemake.utils)
AmbiguousRuleException
ancient() (in module snakemake.io)
AnnotatedString (class in snakemake.io)
AnnotatedStringInterface (class in snakemake.io)
apply_wildcards() (in module snakemake.io)
ArgumentGroup (class in snakemake.common.argparse)
ArgumentParser (class in snakemake.common.argparse)
argvquote() (in module snakemake.utils)
async_run() (in module snakemake.common)
available_cpu_count() (in module snakemake.utils)
AzureFileException
B
BashEncoder (class in snakemake.script)
BashScript (class in snakemake.script)
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)
bytesto() (in module snakemake.common)
C
CacheMissException
change_working_directory() (in module snakemake.executors)
Checkpoint (class in snakemake.checkpoints)
checkpoint_target() (in module snakemake.io)
CheckpointJob (class in snakemake.checkpoints)
Checkpoints (class in snakemake.checkpoints)
CheckSumMismatchException
ChildIOException
CliException
ClusterJobException
cmd_exe_quote() (in module snakemake.utils)
ColorizingStreamHandler (class in snakemake.logging)
Conda (class in snakemake.deployment.conda)
CondaCleanupMode (class in snakemake.deployment.conda)
CondaEnvFileSpec (class in snakemake.deployment.conda)
CondaEnvNameSpec (class in snakemake.deployment.conda)
CondaEnvSpec (class in snakemake.deployment.conda)
containerize() (in module snakemake.deployment.containerize)
contains_wildcard() (in module snakemake.io)
contains_wildcard_constraints() (in module snakemake.io)
CreateCondaEnvironmentException
CreateRuleException
cumsum() (in module snakemake.scheduler)
cut_traceback() (in module snakemake.exceptions)
cwl() (in module snakemake.cwl)
CyclicGraphException
D
DaemonTimer (class in snakemake.benchmark)
dag_to_cwl() (in module snakemake.cwl)
dec_all_methods() (in module snakemake.decorators)
DefaultResources (class in snakemake.resources)
dict_to_key_value_args() (in module snakemake.common)
directory() (in module snakemake.io)
DropboxFileException
DummyRateLimiter (class in snakemake.scheduler)
E
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)
Executor (class in snakemake.executors.dryrun)
(class in snakemake.executors.touch)
ExistsDict (class in snakemake.io)
expand() (in module snakemake.io)
expand_vars_and_user() (in module snakemake.common)
F
find_bash_on_windows() (in module snakemake.utils)
find_extension() (in module snakemake.wrapper)
flag() (in module snakemake.io)
format() (in module snakemake.utils)
format_dict() (in module snakemake.logging)
format_element() (snakemake.utils.SequenceFormatter method)
format_error() (in module snakemake.exceptions)
format_percentage() (in module snakemake.logging)
format_resource_names() (in module snakemake.logging)
format_traceback() (in module snakemake.exceptions)
format_wildcards() (in module snakemake.logging)
from_queue() (in module snakemake.io)
FTPFileException
G
Gather (class in snakemake.common)
generate() (in module snakemake.unit_tests)
GenericSourceFile (class in snakemake.sourcecache)
get_appdirs() (in module snakemake.common)
get_cell_sources() (in module snakemake.notebook)
get_conda_env() (in module snakemake.wrapper)
get_container_image() (in module snakemake.common)
get_default_exec_mode() (in module snakemake.logging)
get_exception_origin() (in module snakemake.exceptions)
get_exec_class() (in module snakemake.notebook)
get_file_hash() (in module snakemake.common)
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_input_function_aux_params() (in module snakemake.common)
get_language() (in module snakemake.script)
get_last_stable_version() (in module snakemake.common)
get_line() (in module snakemake.linting.snakefiles)
get_name_modifier_func() (in module snakemake.modules)
get_path() (in module snakemake.wrapper)
get_script() (in module snakemake.wrapper)
get_snakemake_searchpath_mountpoints() (in module snakemake.deployment.singularity)
get_snakemake_searchpaths() (in module snakemake.common)
get_source() (in module snakemake.script)
get_uuid() (in module snakemake.common)
get_wildcard_constraints() (in module snakemake.io)
get_wildcard_names() (in module snakemake.io)
git_content() (in module snakemake.common.git)
GithubFile (class in snakemake.sourcecache)
GitlabFile (class in snakemake.sourcecache)
glob_wildcards() (in module snakemake.io)
group_into_chunks() (in module snakemake.common)
GroupResources (class in snakemake.resources)
H
HostingProviderFile (class in snakemake.sourcecache)
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)
InOutput (class in snakemake.ruleinfo)
InputFiles (class in snakemake.io)
InputFunctionException
instance() (snakemake.utils.Paramspace method)
instance_patterns (snakemake.utils.Paramspace property)
IOCache (class in snakemake.io)
iocache() (in module snakemake.io)
IOException
IOFile() (in module snakemake.io)
IOFileException
is_callable() (in module snakemake.io)
is_conda_env_file() (in module snakemake.deployment.conda)
is_file_not_found_error() (in module snakemake.exceptions)
is_flagged() (in module snakemake.io)
is_humanfriendly_resource() (in module snakemake.resources)
is_local_file() (in module snakemake.common)
is_mamba_available() (in module snakemake.deployment.conda)
is_namedtuple_instance() (in module snakemake.common)
is_script() (in module snakemake.wrapper)
is_url() (in module snakemake.wrapper)
J
Jinja2Renderer (class in snakemake.template_rendering.jinja2)
job_to_cwl() (in module snakemake.cwl)
JobScheduler (class in snakemake.scheduler)
JuliaEncoder (class in snakemake.script)
JuliaScript (class in snakemake.script)
JupyterNotebook (class in snakemake.notebook)
L
limit() (in module snakemake.io)
linecount() (in module snakemake.utils)
Lint (class in snakemake.linting)
Linter (class in snakemake.linting)
listfiles() (in module snakemake.utils)
load_configfile() (in module snakemake.common.configfile)
local() (in module snakemake.io)
LocalGitFile (class in snakemake.sourcecache)
LocalSourceFile (class in snakemake.sourcecache)
LockException
Log (class in snakemake.io)
log_location() (in module snakemake.common)
log_verbose_traceback() (in module snakemake.exceptions)
Logger (class in snakemake.logging)
LookupError
lutime() (in module snakemake.io)
M
makedirs() (in module snakemake.utils)
mb_to_mib() (in module snakemake.common)
min_version() (in module snakemake.utils)
MissingInputException
MissingOutputException
MissingRuleException
module
snakemake.benchmark
snakemake.checkpoints
snakemake.common
snakemake.common.argparse
snakemake.common.configfile
snakemake.common.git
snakemake.common.tbdstring
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.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.resources
snakemake.ruleinfo
snakemake.rules
snakemake.scheduler
snakemake.script
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)
multiext() (in module snakemake.io)
N
Namedlist (class in snakemake.io)
NCBIFileException
NoRulesException
notebook() (in module snakemake.notebook)
num_if_possible() (in module snakemake.common)
O
os_sync() (in module snakemake.utils)
OutputFiles (class in snakemake.io)
OutputIndex (class in snakemake.output_index)
P
Params (class in snakemake.io)
Paramspace (class in snakemake.utils)
parse_key_value_arg() (in module snakemake.common)
parse_resources() (in module snakemake.resources)
parse_target_jobs_cli_args() (in module snakemake.target_jobs)
parse_uri() (in module snakemake.common)
ParsedResource (class in snakemake.resources)
PathModifier (class in snakemake.path_modifier)
PeriodicityDetector (class in snakemake.io)
PeriodicWildcardError
pipe() (in module snakemake.io)
pretty_print_iofile() (in module snakemake.io)
print_benchmark_records() (in module snakemake.benchmark)
print_exception() (in module snakemake.exceptions)
ProfileConfigFileParser (class in snakemake.profiles)
protected() (in module snakemake.io)
ProtectedOutputException
PythonJupyterNotebook (class in snakemake.notebook)
PythonScript (class in snakemake.script)
Q
QueueInfo (class in snakemake.io)
QuotedFormatter (class in snakemake.utils)
R
R() (in module snakemake.utils)
read_job_properties() (in module snakemake.utils)
regex_from_filepattern() (in module snakemake.io)
register_parser_action() (in module snakemake.common.argparse)
RemoteFileException
remove() (in module snakemake.io)
REncoder (class in snakemake.script)
render_template() (in module snakemake.template_rendering)
repeat() (in module snakemake.io)
report() (in module snakemake.io)
(in module snakemake.utils)
ReportObject (class in snakemake.io)
Resources (class in snakemake.io)
ResourceScopes (class in snakemake.resources)
ResourceScopesException
RJupyterNotebook (class in snakemake.notebook)
RMarkdown (class in snakemake.script)
RScript (class in snakemake.script)
Rule (class in snakemake.rules)
RuleException
RuleInfo (class in snakemake.ruleinfo)
RuleLinter (class in snakemake.linting.rules)
Ruleorder (class in snakemake.rules)
RuleProxy (class in snakemake.rules)
Rules (class in snakemake.common)
RuleTest (class in snakemake.unit_tests)
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)
setup_logger() (in module snakemake.logging)
SFTPFileException
shellcmd() (in module snakemake.deployment.singularity)
simplify_path() (in module snakemake.utils)
Singularity (class in snakemake.deployment.singularity)
SlackLogger (class in snakemake.logging)
smart_join() (in module snakemake.common)
SnakefileLinter (class in snakemake.linting.snakefiles)
Snakemake (class in snakemake.script)
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.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.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.resources
module
snakemake.ruleinfo
module
snakemake.rules
module
snakemake.scheduler
module
snakemake.script
module
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
SourceCache (class in snakemake.sourcecache)
sourcecache_entry() (in module snakemake.io)
SourceFile (class in snakemake.sourcecache)
SourceFileError
SpawnedJobError
split_git_path() (in module snakemake.common.git)
strip_prefix() (in module snakemake.common)
strip_re() (in module snakemake.script)
strip_wildcard_constraints() (in module snakemake.io)
T
TBDString (class in snakemake.common.tbdstring)
temp() (in module snakemake.io)
TemplateRenderer (class in snakemake.template_rendering)
temporary() (in module snakemake.io)
TerminatedException
touch() (in module snakemake.io)
U
unique_justseen() (in module snakemake.common)
UnknownRuleException
unpack() (in module snakemake.io)
update_config() (in module snakemake.utils)
update_lineno() (in module snakemake.exceptions)
update_wildcard_constraints() (in module snakemake.io)
V
validate() (in module snakemake.utils)
W
wait_for_files() (in module snakemake.io)
WebDAVFileException
wildcard_pattern (snakemake.utils.Paramspace property)
WildcardError
Wildcards (class in snakemake.io)
WMSLogger (class in snakemake.logging)
WorkdirHandler (class in snakemake.common.workdir_handler)
WorkflowModifier (class in snakemake.modules)
wrapper() (in module snakemake.wrapper)
write_benchmark_records() (in module snakemake.benchmark)
X
XRootDFileException
Y
YteRenderer (class in snakemake.template_rendering.yte)
Z
ZenodoFileException