Snakemake
5.22.1
Getting started
Installation
Snakemake Tutorial
Short tutorial
Snakemake Executor Tutorials
Executing workflows
Command line interface
Cluster Execution
Cloud execution
Between workflow caching
Interoperability
Defining workflows
Writing Workflows
Rules
Configuration
Modularization
Remote files
Utils
Distribution and Reproducibility
Reports
API Reference
The Snakemake API
Additional utils
Internal API
Project Info
Citing and Citations
More Resources
Frequently Asked Questions
Contributing
Credits
Change Log
License
Snakemake
Docs
»
Index
Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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_default_remote() (snakemake.rules.Rule method)
(snakemake.workflow.Workflow method)
apply_input_function() (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]
attempt() (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
auto_report() (in module snakemake.report)
available_cpu_count() (in module snakemake.utils)
,
[1]
available_protocols() (snakemake.remote.AbstractRemoteProvider method)
(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)
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)
(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.Rule method)
(snakemake.parser.Ruleorder method)
(snakemake.parser.Run method)
(snakemake.parser.Subworkflow 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)
candidate() (snakemake.scheduler.JobScheduler method)
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_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_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
code() (snakemake.persistence.Persistence method)
(snakemake.report.ConfigfileRecord method)
(snakemake.report.RuleRecord method)
code_changed() (snakemake.persistence.Persistence 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)
compare() (snakemake.rules.Ruleorder method)
concrete_files() (snakemake.workflow.Workflow property)
Conda (class in snakemake.parser)
conda() (snakemake.workflow.Workflow method)
conda_cleanup_envs() (snakemake.persistence.Persistence method)
conda_env() (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
conda_env_file() (snakemake.jobs.Job property)
conda_env_path() (snakemake.jobs.Job property)
config() (snakemake.workflow.Workflow property)
Configfile (class in snakemake.parser)
configfile() (snakemake.workflow.Workflow method)
ConfigfileRecord (class in snakemake.report)
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)
contains_wildcard() (in module snakemake.io)
contains_wildcard_constraints() (in module snakemake.io)
cores() (snakemake.workflow.Workflow property)
cpu_seconds (snakemake.benchmark.BenchmarkRecord attribute)
CPUExecutor (class in snakemake.executors)
create_conda_envs() (snakemake.dag.DAG 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.Job attribute)
dag() (in module snakemake.gui)
(snakemake.jobs.GroupJob property)
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)
default (snakemake.common.Mode attribute)
default_jobscript (snakemake.executors.ClusterExecutor attribute)
default_protocol() (snakemake.remote.AbstractRemoteProvider method)
(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)
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.Job attribute)
dynamic_input() (snakemake.jobs.GroupJob property)
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.Rule method)
(snakemake.parser.Run method)
(snakemake.parser.Subworkflow method)
(snakemake.parser.SubworkflowKeywordState 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.ScriptBase 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)
F
fetch_from_ncbi() (snakemake.remote.NCBI.NCBIHelper method)
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)
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_extension() (in module snakemake.wrapper)
finish() (snakemake.dag.DAG method)
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_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
generate_preamble() (snakemake.script.PythonScript static method)
(snakemake.script.RScript 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)
get_args() (in module snakemake.gui)
get_argument_parser() (in module snakemake)
get_batch() (snakemake.dag.Batch method)
get_conda_env() (in module snakemake.wrapper)
get_container_image() (in module snakemake.common)
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_root() (snakemake.io.IOCache 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.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_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_wildcard_constraints() (snakemake.workflow.Workflow method)
GlobalContainer (class in snakemake.parser)
GlobalKeywordState (class in snakemake.parser)
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)
(snakemake.workflow.Workflow method)
group_error() (snakemake.logging.Logger method)
group_info() (snakemake.logging.Logger method)
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)
handler() (snakemake.logging.Logger method)
has_wildcards() (snakemake.rules.Rule method)
HIGHEST_PRIORITY (snakemake.jobs.Job attribute)
host() (snakemake.remote.DomainObject property)
HTTPFileException
httpr() (snakemake.remote.HTTP.RemoteObject method)
I
icon() (snakemake.report.FileRecord property)
id (snakemake.remote.EGA.EGAFileInfo attribute)
ImproperOutputException
ImproperShadowException
in_inventory() (snakemake.io.IOCache method)
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.Job attribute)
input() (snakemake.jobs.GroupJob property)
(snakemake.persistence.Persistence method)
(snakemake.report.RuleRecord property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
(snakemake.workflow.Workflow method)
input_changed() (snakemake.persistence.Persistence method)
input_maxtime() (snakemake.jobs.Job property)
inputfile() (snakemake.workflow.Workflow method)
InputFiles (class in snakemake.io)
InputFunctionException
inputsize() (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
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_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() (in module snakemake.wrapper)
(snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.workflow.Workflow method)
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() (in module snakemake.wrapper)
(snakemake.jobs.Job property)
(snakemake.rules.Rule property)
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_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() (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)
jobid() (snakemake.dag.DAG method)
(snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
jobname (snakemake.executors.TibannaJob attribute)
JobRecord (class in snakemake.report)
jobs (snakemake.jobs.GroupJob attribute)
jobs() (snakemake.dag.DAG property)
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.Envvars property)
(snakemake.parser.GlobalContainer property)
(snakemake.parser.GlobalSingularity property)
(snakemake.parser.GlobalWildcardConstraints property)
(snakemake.parser.KeywordState property)
(snakemake.parser.Singularity property)
(snakemake.parser.WildcardConstraints property)
KeywordState (class in snakemake.parser)
kill() (snakemake.shell.shell class method)
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.AbstractRemoteObject method)
(snakemake.remote.dropbox.RemoteObject property)
(snakemake.remote.HTTP.RemoteObject property)
(snakemake.remote.NCBI.RemoteObject property)
(snakemake.remote.S3.RemoteObject property)
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)
local_file() (snakemake.remote.AbstractRemoteObject method)
local_input() (snakemake.jobs.Job property)
local_needrun_jobs() (snakemake.dag.DAG property)
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() (in module snakemake.gui)
(snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.persistence.Persistence method)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
(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)
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]
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.jobs.GroupJob method)
Message (class in snakemake.parser)
message() (snakemake.jobs.Job property)
(snakemake.workflow.Workflow method)
messages() (snakemake.exceptions.RuleException property)
metadata() (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.Job method)
(snakemake.jobs.Reason property)
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)
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
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)
multiext() (in module snakemake.io)
N
name() (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.parser.Rule method)
(snakemake.parser.Subworkflow method)
(snakemake.remote.AbstractRemoteObject method)
(snakemake.remote.DomainObject property)
(snakemake.remote.dropbox.RemoteObject property)
(snakemake.remote.S3.RemoteObject property)
(snakemake.report.FileRecord property)
Namedlist (class in snakemake.io)
NCBIFileException
NCBIHelper (class in snakemake.remote.NCBI)
needrun() (snakemake.dag.DAG method)
needrun_jobs() (snakemake.dag.DAG property)
needs_inventory() (snakemake.io.IOCache method)
needs_singularity() (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
new() (snakemake.jobs.GroupJobFactory method)
(snakemake.jobs.JobFactory 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.Job attribute)
output() (snakemake.jobs.GroupJob property)
(snakemake.report.RuleRecord property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
(snakemake.workflow.Workflow method)
output_mintime() (snakemake.jobs.Job property)
output_mintime_local() (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.persistence.Persistence method)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
(snakemake.workflow.Workflow method)
params_changed() (snakemake.persistence.Persistence method)
parse() (in module snakemake.parser)
parse_accession_str() (snakemake.remote.NCBI.NCBIHelper method)
parse_batch() (in module snakemake)
parse_config() (in module snakemake)
parse_key_value_arg() (in module snakemake)
parse_set_threads() (in module snakemake)
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)
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)
port() (snakemake.remote.DomainObject property)
postprocess() (snakemake.dag.DAG method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
prefix (snakemake.parser.KeywordState 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.dag.DAG method)
(snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(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
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_secret() (snakemake.executors.KubernetesExecutor method)
register_wildcards() (snakemake.rules.Rule method)
remote() (snakemake.remote.AbstractRemoteObject method)
(snakemake.remote.AbstractRemoteProvider 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)
RESET_SEQ (snakemake.logging.ColorizingStreamHandler attribute)
Resources (class in snakemake.io)
(class in snakemake.parser)
resources() (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(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)
RuleInfo (class in snakemake.workflow)
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.workflow)
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)
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)
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)
SequenceFormatter (class in snakemake.utils)
,
[1]
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_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)
(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.remote.EGA.EGAFileInfo attribute)
size() (snakemake.io.InputFiles property)
(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)
Snakefile (class in snakemake.parser)
snakefile() (snakemake.workflow.Subworkflow 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
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.SubworkflowKeywordState 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)
StaticRemoteObjectProxy (class in snakemake.remote)
Stats (class in snakemake.stats)
stats() (snakemake.dag.DAG method)
(snakemake.scheduler.JobScheduler property)
status (snakemake.remote.EGA.EGAFileInfo attribute)
status() (in module snakemake.gui)
StopAutomaton
strip_prefix() (in module snakemake.common)
strip_wildcard_constraints() (in module snakemake.io)
subautomata (snakemake.parser.Python attribute)
(snakemake.parser.Rule attribute)
(snakemake.parser.Subworkflow attribute)
(snakemake.parser.TokenAutomaton 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.workflow.Subworkflow method)
targetfile (snakemake.jobs.Job attribute)
targets() (in module snakemake.gui)
(snakemake.workflow.Subworkflow method)
TBDInt (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)
(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)
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.persistence.Persistence method)
(snakemake.remote.NCBI.RemoteObject property)
(snakemake.rules.Rule property)
(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)
(snakemake.workflow.Workflow method)
wildcard_names() (snakemake.rules.Rule property)
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)
work() (snakemake.benchmark.BenchmarkTimer method)
(snakemake.benchmark.ScheduledPeriodicTimer method)
Workdir (class in snakemake.parser)
workdir() (snakemake.workflow.Subworkflow property)
(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.ScriptBase method)
X
XRootDFileException
Y
YELLOW (snakemake.logging.ColorizingStreamHandler attribute)
yield_indent() (snakemake.parser.KeywordState method)