Snakemake
v7.2.1
Getting started
Installation
Snakemake Tutorial
Short tutorial
Snakemake Executor Tutorials
Best practices
Executing workflows
Command line interface
Cluster Execution
Cloud execution
Job Grouping
Between workflow caching
Interoperability
Monitoring
Defining workflows
Writing Workflows
Snakefiles and Rules
Configuration
Modularization
Remote files
Utils
Distribution and Reproducibility
Reports
Automatically generating unit tests
Integrating foreign workflow management systems
API Reference
The Snakemake API
Additional utils
Internal API
Project Info
Citing and Citations
More Resources
Frequently Asked Questions
Contributing
Credits
Changelog
License
Snakemake
Docs
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
A
AbstractCmd (class in snakemake.parser)
AbstractExecutor (class in snakemake.executors)
AbstractJob (class in snakemake.jobs)
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)
AlwaysQuotedFormatter (class in snakemake.utils)
,
[1]
AmbiguousRuleException
ancient() (in module snakemake.io)
AnnotatedString (class in snakemake.io)
apply_input_function() (snakemake.rules.Rule method)
apply_path_modifier() (snakemake.rules.Rule method)
apply_wildcards() (in module snakemake.io)
archive() (snakemake.dag.DAG method)
archive_conda_env() (snakemake.jobs.Job method)
args (snakemake.parser.DecoratorKeywordState attribute)
(snakemake.parser.OnError attribute)
(snakemake.parser.OnStart attribute)
(snakemake.parser.OnSuccess attribute)
args() (snakemake.parser.AbstractCmd method)
(snakemake.parser.CWL method)
(snakemake.parser.Notebook method)
(snakemake.parser.Script method)
(snakemake.parser.Shell method)
(snakemake.parser.TemplateEngine method)
(snakemake.parser.Wrapper method)
argvquote() (in module snakemake.utils)
,
[1]
async_run() (in module snakemake.common)
attempt (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
auto_report() (in module snakemake.report)
available_cpu_count() (in module snakemake.utils)
,
[1]
AzureFileException
B
b64id (snakemake.jobs.Job property)
bash_completion() (in module snakemake)
Batch (class in snakemake.dag)
bench_record (snakemake.benchmark.BenchmarkTimer attribute)
Benchmark (class in snakemake.parser)
benchmark (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
benchmark() (snakemake.workflow.Workflow method)
BENCHMARK_INTERVAL (in module snakemake.benchmark)
BENCHMARK_INTERVAL_SHORT (in module snakemake.benchmark)
benchmark_repeats (snakemake.jobs.Job property)
benchmarked() (in module snakemake.benchmark)
BenchmarkRecord (class in snakemake.benchmark)
BenchmarkTimer (class in snakemake.benchmark)
bfs() (snakemake.dag.DAG method)
BLACK (snakemake.logging.ColorizingStreamHandler attribute)
block() (snakemake.parser.KeywordState method)
block_content() (snakemake.parser.AbstractCmd method)
(snakemake.parser.KeywordState method)
(snakemake.parser.Localrules method)
(snakemake.parser.Module method)
(snakemake.parser.Rule method)
(snakemake.parser.Ruleorder method)
(snakemake.parser.Run method)
(snakemake.parser.Subworkflow method)
(snakemake.parser.UseRule method)
BLUE (snakemake.logging.ColorizingStreamHandler attribute)
BOLD_SEQ (snakemake.logging.ColorizingStreamHandler attribute)
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 property)
(snakemake.executors.GenericClusterJob property)
(snakemake.executors.KubernetesJob property)
(snakemake.executors.SynchronousClusterJob property)
(snakemake.executors.TibannaJob property)
can_color_tty() (snakemake.logging.ColorizingStreamHandler method)
cancel() (snakemake.benchmark.DaemonTimer method)
(snakemake.benchmark.ScheduledPeriodicTimer method)
(snakemake.executors.AbstractExecutor method)
(snakemake.executors.ClusterExecutor method)
(snakemake.executors.CPUExecutor method)
(snakemake.executors.DRMAAExecutor method)
(snakemake.executors.GenericClusterExecutor method)
(snakemake.executors.KubernetesExecutor method)
(snakemake.executors.SynchronousClusterExecutor method)
(snakemake.executors.TibannaExecutor method)
CandidateGroup (class in snakemake.dag)
caption (snakemake.io.ReportObject property)
Category (class in snakemake.report)
category (snakemake.io.ReportObject property)
change_working_directory() (in module snakemake.executors)
check() (snakemake.workflow.Workflow method)
check_and_touch_output() (snakemake.dag.DAG method)
check_caching() (snakemake.rules.Rule method)
check_directory_outputs() (snakemake.dag.DAG method)
check_dynamic() (snakemake.dag.DAG method)
check_incomplete() (snakemake.dag.DAG method)
check_localrules() (snakemake.workflow.Workflow method)
check_output() (snakemake.shell.shell class method)
check_output_duplicates() (snakemake.rules.Rule method)
check_periodic_wildcards() (snakemake.dag.DAG method)
check_protected_output() (snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
check_response() (snakemake.logging.WMSLogger method)
check_source_sizes() (snakemake.workflow.Workflow method)
check_wildcards() (snakemake.rules.Rule method)
Checkpoint (class in snakemake.checkpoints)
(class in snakemake.parser)
checkpoint_jobs (snakemake.dag.DAG property)
checkpoint_target() (in module snakemake.io)
CheckpointJob (class in snakemake.checkpoints)
Checkpoints (class in snakemake.checkpoints)
checkpoints (snakemake.checkpoints.Checkpoint attribute)
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_remote() (snakemake.jobs.Job method)
close_remote_objects() (snakemake.dag.DAG method)
cluster (snakemake.common.Mode attribute)
cluster_params() (snakemake.executors.ClusterExecutor method)
cluster_wildcards() (snakemake.executors.ClusterExecutor method)
ClusterExecutor (class in snakemake.executors)
ClusterJobException
cmd_exe_quote() (in module snakemake.utils)
,
[1]
code (snakemake.report.RuleRecord property)
code() (snakemake.persistence.Persistence method)
(snakemake.report.ConfigfileRecord method)
code_changed() (snakemake.persistence.Persistence method)
collect_mtime() (snakemake.io.IOCache method)
collect_potential_dependencies() (snakemake.dag.DAG method)
colon() (snakemake.parser.KeywordState method)
COLOR_SEQ (snakemake.logging.ColorizingStreamHandler attribute)
ColorizingStreamHandler (class in snakemake.logging)
colors (snakemake.logging.ColorizingStreamHandler attribute)
combine_preamble_and_source() (snakemake.script.RustScript method)
compare() (snakemake.rules.Ruleorder method)
concrete_files (snakemake.workflow.Workflow property)
Conda (class in snakemake.parser)
conda() (snakemake.workflow.Workflow method)
conda_base_path (snakemake.workflow.Workflow property)
conda_block_conflicting_envvars (snakemake.shell.shell attribute)
conda_cleanup_envs() (snakemake.persistence.Persistence method)
conda_env (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
conda_env_spec (snakemake.jobs.Job property)
config (snakemake.workflow.Workflow property)
Configfile (class in snakemake.parser)
configfile() (snakemake.workflow.Workflow method)
ConfigfileRecord (class in snakemake.report)
consume() (snakemake.parser.TokenAutomaton method)
Container (class in snakemake.parser)
container() (snakemake.workflow.Workflow method)
container_img (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
container_img_path (snakemake.jobs.Job property)
container_img_url (snakemake.jobs.Job property)
containerize() (snakemake.workflow.Workflow method)
Containerized (class in snakemake.parser)
containerized() (snakemake.workflow.Workflow method)
contains_wildcard() (in module snakemake.io)
contains_wildcard_constraints() (in module snakemake.io)
cores (snakemake.workflow.Workflow property)
cpu_time (snakemake.benchmark.BenchmarkRecord attribute)
cpu_usages (snakemake.benchmark.BenchmarkRecord attribute)
CPUExecutor (class in snakemake.executors)
create_conda_envs() (snakemake.dag.DAG method)
create_workflow() (snakemake.logging.WMSLogger method)
CreateCondaEnvironmentException
CreateRuleException
cumsum() (in module snakemake.scheduler)
current_basedir (snakemake.workflow.Workflow property)
cut_traceback() (in module snakemake.exceptions)
CWL (class in snakemake.parser)
cwl() (in module snakemake.cwl)
(snakemake.workflow.Workflow method)
CYAN (snakemake.logging.ColorizingStreamHandler attribute)
CyclicGraphException
D
d3dag() (snakemake.dag.DAG method)
(snakemake.logging.Logger method)
DaemonTimer (class in snakemake.benchmark)
DAG (class in snakemake.dag)
dag (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job attribute)
dag_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)
deactivate() (snakemake.io.IOCache method)
deactivate_cache() (snakemake.persistence.Persistence method)
debug() (snakemake.logging.Logger method)
dec_all_methods() (in module snakemake.decorators)
decorate() (snakemake.logging.ColorizingStreamHandler method)
decorate_end() (snakemake.parser.AbstractCmd method)
(snakemake.parser.KeywordState method)
decorator (snakemake.parser.DecoratorKeywordState attribute)
(snakemake.parser.OnError attribute)
(snakemake.parser.OnStart attribute)
(snakemake.parser.OnSuccess attribute)
DecoratorKeywordState (class in snakemake.parser)
dedent (snakemake.parser.Rule property)
(snakemake.parser.TokenAutomaton property)
(snakemake.parser.UseRule property)
default (snakemake.common.Mode attribute)
default_dependencies() (snakemake.script.RustScript static method)
default_features() (snakemake.script.RustScript static method)
default_jobscript (snakemake.executors.ClusterExecutor attribute)
default_target_rule() (snakemake.workflow.Workflow method)
DefaultTarget (class in snakemake.parser)
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)
dot() (snakemake.dag.DAG 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)
DropboxFileException
DryrunExecutor (class in snakemake.executors)
DummyRateLimiter (class in snakemake.scheduler)
dynamic() (in module snakemake.io)
(snakemake.dag.DAG method)
dynamic_branch() (snakemake.rules.Rule method)
dynamic_input (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job attribute)
dynamic_output (snakemake.jobs.Job attribute)
dynamic_output_jobs (snakemake.dag.DAG property)
dynamic_wildcards (snakemake.jobs.Job property)
E
editable (snakemake.script.ScriptBase attribute)
effective_indent (snakemake.parser.TokenAutomaton property)
EmbeddedFigure (class in snakemake.report)
EmbeddedImage (class in snakemake.report)
EmbeddedMixin (class in snakemake.report)
emit() (snakemake.logging.ColorizingStreamHandler method)
encode_dict() (snakemake.script.JuliaEncoder class method)
(snakemake.script.REncoder class method)
encode_items() (snakemake.script.JuliaEncoder class method)
(snakemake.script.REncoder class method)
encode_list() (snakemake.script.JuliaEncoder class method)
(snakemake.script.REncoder class method)
encode_namedlist() (snakemake.script.JuliaEncoder class method)
(snakemake.script.REncoder class method)
encode_numeric() (snakemake.script.REncoder class method)
encode_positional_items() (snakemake.script.JuliaEncoder class method)
encode_value() (snakemake.script.JuliaEncoder class method)
(snakemake.script.REncoder class method)
end() (snakemake.parser.AbstractCmd method)
(snakemake.parser.DecoratorKeywordState method)
(snakemake.parser.KeywordState method)
(snakemake.parser.Module method)
(snakemake.parser.Rule method)
(snakemake.parser.Run method)
(snakemake.parser.SectionKeywordState method)
(snakemake.parser.Subworkflow method)
(snakemake.parser.UseRule method)
end_func (snakemake.parser.AbstractCmd attribute)
(snakemake.parser.CWL attribute)
(snakemake.parser.Notebook attribute)
(snakemake.parser.Script attribute)
(snakemake.parser.Shell attribute)
(snakemake.parser.TemplateEngine 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 property)
(snakemake.executors.GenericClusterJob property)
(snakemake.executors.KubernetesJob property)
(snakemake.executors.SynchronousClusterJob property)
(snakemake.executors.TibannaJob property)
evaluate() (snakemake.script.ScriptBase method)
exec_arn (snakemake.executors.TibannaJob property)
executable() (snakemake.shell.shell class method)
execute() (snakemake.workflow.Workflow method)
execute_script() (snakemake.script.JuliaScript method)
(snakemake.script.PythonScript method)
(snakemake.script.RMarkdown method)
(snakemake.script.RScript method)
(snakemake.script.RustScript method)
(snakemake.script.ScriptBase method)
executor_error_callback() (snakemake.scheduler.JobScheduler method)
existing_output (snakemake.jobs.Job property)
existing_remote_input (snakemake.jobs.Job property)
existing_remote_output (snakemake.jobs.Job property)
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_labels() (in module snakemake.report)
expand_log() (snakemake.rules.Rule method)
expand_output() (snakemake.rules.Rule method)
expand_params() (snakemake.rules.Rule method)
expand_report_argument() (in module snakemake.report)
expand_resources() (snakemake.rules.Rule method)
expanded_output (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
external_jobids() (snakemake.persistence.Persistence method)
extract_manifest() (snakemake.script.RustScript static method)
F
file (snakemake.dag.PotentialDependency property)
file2jobs() (snakemake.dag.DAG method)
file_stats (snakemake.stats.Stats property)
filegraph_dot() (snakemake.dag.DAG method)
filename (snakemake.report.FileRecord property)
FileRecord (class in snakemake.report)
files (snakemake.persistence.Persistence property)
files_to_download (snakemake.jobs.Job property)
files_to_upload (snakemake.jobs.Job property)
finalize() (snakemake.jobs.GroupJob method)
find_bash_on_windows() (in module snakemake.utils)
,
[1]
find_extension() (in module snakemake.wrapper)
finish() (snakemake.dag.DAG method)
finished (snakemake.jobs.Reason attribute)
finished() (snakemake.dag.DAG method)
(snakemake.persistence.Persistence method)
finished_jobs (snakemake.dag.DAG property)
first_time (snakemake.benchmark.BenchmarkRecord attribute)
flag() (in module snakemake.io)
forced (snakemake.jobs.Reason attribute)
format() (in module snakemake.utils)
,
[1]
format_arg() (snakemake.exceptions.WorkflowError static method)
format_dict() (in module snakemake.logging)
format_element() (snakemake.utils.SequenceFormatter method)
,
[1]
format_error() (in module snakemake.exceptions)
format_field() (snakemake.utils.AlwaysQuotedFormatter method)
(snakemake.utils.QuotedFormatter method)
(snakemake.utils.SequenceFormatter method)
format_files() (in module snakemake.jobs)
format_job() (snakemake.executors.ClusterExecutor method)
format_job_pattern() (snakemake.executors.RealExecutor method)
format_percentage() (in module snakemake.logging)
format_resource_names() (in module snakemake.logging)
format_resources() (in module snakemake.logging)
format_tokens() (in module snakemake.parser)
format_traceback() (in module snakemake.exceptions)
format_wildcards() (in module snakemake.logging)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
FTPFileException
G
Gather (class in snakemake.common)
generate_parser_metadata() (in module snakemake)
generate_preamble() (snakemake.script.PythonScript static method)
(snakemake.script.RScript static method)
(snakemake.script.RustScript static method)
GenericClusterExecutor (class in snakemake.executors)
GenericClusterJob (class in snakemake.executors)
get() (snakemake.checkpoints.Checkpoint method)
(snakemake.io.Namedlist method)
get_additional_args() (snakemake.executors.RealExecutor method)
get_appdirs() (in module snakemake.common)
get_argument_parser() (in module snakemake)
get_batch() (snakemake.dag.Batch method)
get_behavior_args() (snakemake.executors.AbstractExecutor method)
get_conda_env() (in module snakemake.wrapper)
get_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_flag_value() (in module snakemake.io)
get_function_params() (in module snakemake.common)
get_git_root() (in module snakemake.io)
get_git_root_parent_directory() (in module snakemake.io)
get_header() (snakemake.benchmark.BenchmarkRecord class method)
get_input_function_aux_params() (in module snakemake.common)
get_job_group() (snakemake.dag.DAG 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_local_groupid_arg() (snakemake.executors.AbstractExecutor method)
get_logfile() (snakemake.logging.Logger method)
get_outputs_with_changes() (snakemake.dag.DAG method)
get_path() (in module snakemake.wrapper)
get_preamble() (snakemake.script.JuliaScript method)
(snakemake.script.PythonScript method)
(snakemake.script.RMarkdown method)
(snakemake.script.RScript method)
(snakemake.script.RustScript method)
(snakemake.script.ScriptBase method)
get_profile_file() (in module snakemake)
get_resource_as_string() (in module snakemake.report)
get_rule() (snakemake.workflow.Workflow method)
get_script() (in module snakemake.wrapper)
get_set_resources_args() (snakemake.executors.AbstractExecutor method)
get_set_scatter_args() (snakemake.executors.AbstractExecutor method)
get_set_threads_args() (snakemake.executors.AbstractExecutor method)
get_source() (in module snakemake.script)
get_sources() (snakemake.workflow.Workflow method)
get_targets() (snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
get_uuid() (in module snakemake.common)
get_wait_for_files() (snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
get_wildcard_len() (snakemake.rules.Rule static method)
get_wildcard_names() (in module snakemake.io)
get_wildcards() (snakemake.rules.Rule method)
git_content() (in module snakemake.io)
glob_wildcards() (in module snakemake.io)
global_container() (snakemake.workflow.Workflow method)
global_containerized() (snakemake.workflow.Workflow method)
global_wildcard_constraints() (snakemake.workflow.Workflow method)
GlobalContainer (class in snakemake.parser)
GlobalContainerized (class in snakemake.parser)
GlobalKeywordState (class in snakemake.parser)
globals (snakemake.workflow.Workflow property)
GlobalSingularity (class in snakemake.parser)
GlobalWildcardConstraints (class in snakemake.parser)
GREEN (snakemake.logging.ColorizingStreamHandler attribute)
Group (class in snakemake.parser)
group (snakemake.jobs.Job property)
group() (snakemake.workflow.Workflow method)
group_error() (snakemake.logging.Logger method)
group_info() (snakemake.logging.Logger method)
group_into_chunks() (in module snakemake.common)
groupid (snakemake.jobs.GroupJob attribute)
GroupJob (class in snakemake.jobs)
GroupJobFactory (class in snakemake.jobs)
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_and_services() (snakemake.dag.DAG method)
handle_protected() (snakemake.dag.DAG method)
handle_remote() (snakemake.dag.DAG method)
(snakemake.executors.TibannaExecutor method)
handle_temp() (snakemake.dag.DAG method)
handle_touch() (snakemake.dag.DAG method)
handle_with() (snakemake.parser.UseRule method)
handler() (snakemake.logging.Logger method)
Handover (class in snakemake.parser)
handover() (snakemake.workflow.Workflow method)
has_wildcards() (snakemake.rules.Rule method)
HIGHEST_PRIORITY (snakemake.jobs.Job attribute)
htmlindex (snakemake.io.ReportObject property)
HTTPFileException
I
icon (snakemake.report.FileRecord property)
ImproperOutputException
ImproperShadowException
in_omitfrom() (snakemake.dag.DAG method)
in_until() (snakemake.dag.DAG method)
Include (class in snakemake.parser)
include() (snakemake.workflow.Workflow method)
incomplete() (snakemake.persistence.Persistence method)
incomplete_external_jobid() (snakemake.dag.DAG method)
incomplete_files (snakemake.dag.DAG property)
incomplete_input_expand (snakemake.jobs.Job attribute)
incomplete_output (snakemake.jobs.Reason property)
IncompleteCheckpointException
IncompleteFilesException
indentation() (snakemake.parser.TokenAutomaton method)
info() (snakemake.logging.Logger method)
init() (snakemake.dag.DAG method)
Input (class in snakemake.parser)
input (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job attribute)
(snakemake.report.RuleRecord property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
input() (snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
input_changed() (snakemake.persistence.Persistence method)
inputfile() (snakemake.workflow.Workflow method)
InputFiles (class in snakemake.io)
InputFunctionException
inputsize (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
instance() (snakemake.utils.Paramspace method)
,
[1]
instance_patterns (snakemake.utils.Paramspace property)
,
[1]
io_in (snakemake.benchmark.BenchmarkRecord attribute)
io_out (snakemake.benchmark.BenchmarkRecord attribute)
IOCache (class in snakemake.io)
IOException
IOFile() (in module snakemake.io)
IOFileException
is_batch_rule() (snakemake.dag.DAG method)
is_block_end() (snakemake.parser.AbstractCmd method)
(snakemake.parser.KeywordState method)
(snakemake.parser.Run method)
is_branched (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
is_cached_rule() (snakemake.workflow.Workflow method)
is_callable() (in module snakemake.io)
is_checkpoint (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
is_colon() (in module snakemake.parser)
is_comma() (in module snakemake.parser)
is_comment() (in module snakemake.parser)
is_containerized (snakemake.jobs.Job property)
is_cwl (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
is_dedent() (in module snakemake.parser)
is_edit_notebook_job() (snakemake.dag.DAG method)
is_eof() (in module snakemake.parser)
is_final (snakemake.dag.Batch property)
is_flagged() (in module snakemake.io)
is_git_path() (in module snakemake.wrapper)
is_greater() (in module snakemake.parser)
is_group() (snakemake.jobs.AbstractJob method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
is_img (snakemake.report.FileRecord property)
is_indent() (in module snakemake.parser)
is_local (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
is_local() (in module snakemake.wrapper)
(snakemake.workflow.Workflow method)
is_local_file() (in module snakemake.common)
is_name() (in module snakemake.parser)
is_newline() (in module snakemake.parser)
is_norun (snakemake.jobs.Job property)
is_notebook (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
is_op() (in module snakemake.parser)
is_periodic() (snakemake.io.PeriodicityDetector method)
is_pipe (snakemake.jobs.Job property)
is_producer() (snakemake.rules.Rule method)
is_rule() (snakemake.workflow.Workflow method)
is_run (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
is_script (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
is_script() (in module snakemake.wrapper)
is_service (snakemake.jobs.Job 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_template_engine (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
is_text (snakemake.report.FileRecord property)
is_tty (snakemake.logging.ColorizingStreamHandler property)
is_updated (snakemake.jobs.GroupJob property)
is_url() (in module snakemake.wrapper)
is_valid() (snakemake.jobs.Job method)
is_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 property)
(snakemake.executors.GenericClusterJob property)
(snakemake.executors.KubernetesJob property)
(snakemake.executors.SynchronousClusterJob property)
(snakemake.executors.TibannaJob property)
job_args_and_prepare() (snakemake.executors.CPUExecutor method)
job_error() (snakemake.logging.Logger method)
job_finished() (snakemake.logging.Logger method)
job_info() (snakemake.logging.Logger method)
job_reward() (snakemake.scheduler.JobScheduler method)
job_selector_greedy() (snakemake.scheduler.JobScheduler method)
job_selector_ilp() (snakemake.scheduler.JobScheduler method)
job_to_cwl() (in module snakemake.cwl)
job_weight() (snakemake.scheduler.JobScheduler method)
JobFactory (class in snakemake.jobs)
jobfailed (snakemake.executors.GenericClusterJob property)
jobfiles() (in module snakemake.jobs)
jobfinished (snakemake.executors.GenericClusterJob property)
jobid (snakemake.executors.DRMAAClusterJob property)
(snakemake.executors.GenericClusterJob property)
(snakemake.executors.KubernetesJob property)
(snakemake.executors.SynchronousClusterJob property)
(snakemake.executors.TibannaJob property)
(snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
jobid() (snakemake.dag.DAG method)
jobname (snakemake.executors.TibannaJob property)
JobRecord (class in snakemake.report)
jobs (snakemake.dag.DAG property)
(snakemake.dag.PotentialDependency property)
(snakemake.jobs.GroupJob attribute)
JobScheduler (class in snakemake.scheduler)
jobscript (snakemake.executors.DRMAAClusterJob property)
(snakemake.executors.GenericClusterJob property)
(snakemake.executors.KubernetesJob property)
(snakemake.executors.SynchronousClusterJob property)
JuliaEncoder (class in snakemake.script)
JuliaScript (class in snakemake.script)
K
keys() (snakemake.io.Namedlist method)
keyword (snakemake.parser.Cache property)
(snakemake.parser.DefaultTarget property)
(snakemake.parser.Envvars property)
(snakemake.parser.GlobalContainer property)
(snakemake.parser.GlobalContainerized property)
(snakemake.parser.GlobalSingularity property)
(snakemake.parser.GlobalWildcardConstraints property)
(snakemake.parser.KeywordState property)
(snakemake.parser.ModuleMetaWrapper property)
(snakemake.parser.ModuleReplacePrefix property)
(snakemake.parser.ModuleSkipValidation property)
(snakemake.parser.Pepfile property)
(snakemake.parser.Singularity property)
(snakemake.parser.WildcardConstraints property)
KeywordState (class in snakemake.parser)
kill() (snakemake.shell.shell class method)
known (snakemake.dag.PotentialDependency property)
kubejob (snakemake.executors.KubernetesJob property)
KubernetesExecutor (class in snakemake.executors)
KubernetesJob (class in snakemake.executors)
L
labels (snakemake.io.ReportObject property)
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_resources() (snakemake.workflow.Workflow method)
list_rules() (snakemake.workflow.Workflow method)
list_untracked() (snakemake.dag.DAG method)
listfiles() (in module snakemake.utils)
,
[1]
load_configfile() (in module snakemake.io)
local() (in module snakemake.io)
(snakemake.io.Mtime method)
local_input (snakemake.jobs.Job property)
local_needrun_jobs (snakemake.dag.DAG property)
local_or_remote() (snakemake.io.Mtime method)
local_output (snakemake.jobs.Job property)
local_path (snakemake.script.ScriptBase property)
Localrules (class in snakemake.parser)
localrules() (snakemake.workflow.Workflow method)
location() (snakemake.logging.Logger method)
lock() (snakemake.persistence.Persistence method)
lock_warn_only() (snakemake.persistence.Persistence method)
locked (snakemake.persistence.Persistence property)
Log (class in snakemake.io)
(class in snakemake.parser)
log (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
log() (snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
log_error() (snakemake.jobs.AbstractJob method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
log_fmt_shell() (snakemake.script.Snakemake method)
log_handler() (snakemake.logging.SlackLogger method)
(snakemake.logging.WMSLogger method)
log_info() (snakemake.jobs.AbstractJob method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
log_location() (in module snakemake.common)
log_verbose_traceback() (in module snakemake.exceptions)
logfile_hint() (snakemake.logging.Logger method)
Logger (class in snakemake.logging)
lutime() (in module snakemake.io)
M
MAGENTA (snakemake.logging.ColorizingStreamHandler attribute)
main() (in module snakemake)
make_tibanna_input() (snakemake.executors.TibannaExecutor method)
makedirs() (in module snakemake.utils)
,
[1]
mark_finished() (snakemake.jobs.Reason method)
match() (snakemake.output_index.OutputIndex method)
max_pss (snakemake.benchmark.BenchmarkRecord attribute)
max_rss (snakemake.benchmark.BenchmarkRecord attribute)
max_uss (snakemake.benchmark.BenchmarkRecord attribute)
max_vms (snakemake.benchmark.BenchmarkRecord attribute)
merge() (snakemake.dag.CandidateGroup method)
(snakemake.jobs.GroupJob method)
Message (class in snakemake.parser)
message (snakemake.jobs.Job property)
message() (snakemake.workflow.Workflow method)
messages (snakemake.exceptions.RuleException property)
metadata() (snakemake.persistence.Persistence method)
migrate_v1_to_v2() (snakemake.persistence.Persistence method)
mime_from_file() (in module snakemake.report)
min_version() (in module snakemake.utils)
,
[1]
missing_input (snakemake.jobs.Job property)
missing_output (snakemake.jobs.Reason property)
missing_output() (snakemake.jobs.Job method)
missing_remote_input (snakemake.jobs.Job property)
missing_remote_output (snakemake.jobs.Job property)
missing_temp() (snakemake.dag.DAG method)
MissingInputException
MissingOutputException
MissingRuleException
Mode (class in snakemake.common)
modifier (snakemake.workflow.Workflow property)
module
snakemake
snakemake.benchmark
snakemake.checkpoints
snakemake.common
snakemake.cwl
snakemake.dag
snakemake.decorators
snakemake.exceptions
snakemake.executors
snakemake.io
snakemake.jobs
snakemake.logging
snakemake.output_index
snakemake.parser
snakemake.persistence
snakemake.report
snakemake.rules
snakemake.scheduler
snakemake.script
snakemake.shell
snakemake.stats
snakemake.utils
,
[1]
snakemake.workflow
snakemake.wrapper
Module (class in snakemake.parser)
module() (snakemake.workflow.Workflow method)
ModuleConfig (class in snakemake.parser)
ModuleKeywordState (class in snakemake.parser)
ModuleMetaWrapper (class in snakemake.parser)
ModulePrefix (class in snakemake.parser)
ModuleReplacePrefix (class in snakemake.parser)
ModuleSkipValidation (class in snakemake.parser)
ModuleSnakefile (class in snakemake.parser)
Mtime (class in snakemake.io)
mtime_inventory() (snakemake.io.IOCache method)
multiext() (in module snakemake.io)
N
Name (class in snakemake.parser)
name (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.report.FileRecord property)
name() (snakemake.parser.Module method)
(snakemake.parser.Rule method)
(snakemake.parser.Subworkflow method)
(snakemake.workflow.Workflow method)
Namedlist (class in snakemake.io)
NCBIFileException
needrun() (snakemake.dag.DAG method)
needrun_jobs (snakemake.dag.DAG property)
needs_singularity (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
new() (snakemake.jobs.GroupJobFactory method)
(snakemake.jobs.JobFactory method)
new_from() (snakemake.io.AnnotatedString method)
new_job() (snakemake.dag.DAG method)
new_wildcards() (snakemake.dag.DAG method)
newversion_files (snakemake.dag.DAG property)
nodes (snakemake.workflow.Workflow property)
noio (snakemake.jobs.Reason attribute)
noneedrun_finished() (snakemake.dag.DAG method)
noop() (snakemake.persistence.Persistence method)
nooutput (snakemake.jobs.Reason attribute)
NoRulesException
norun() (snakemake.workflow.Workflow method)
not_iterable() (in module snakemake.io)
Notebook (class in snakemake.parser)
notebook() (snakemake.workflow.Workflow method)
num_if_possible() (in module snakemake.common)
O
obj_cache (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
omitfrom_jobs() (snakemake.dag.DAG method)
OnError (class in snakemake.parser)
onerror() (snakemake.workflow.Workflow method)
OnStart (class in snakemake.parser)
onstart() (snakemake.workflow.Workflow method)
OnSuccess (class in snakemake.parser)
onsuccess() (snakemake.workflow.Workflow method)
open_jobs (snakemake.scheduler.JobScheduler property)
os_sync() (in module snakemake.utils)
,
[1]
Output (class in snakemake.parser)
output (snakemake.checkpoints.CheckpointJob attribute)
(snakemake.jobs.GroupJob property)
(snakemake.jobs.Job attribute)
(snakemake.report.RuleRecord property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
output() (snakemake.workflow.Workflow method)
output_mintime (snakemake.jobs.Job property)
OutputFiles (class in snakemake.io)
OutputIndex (class in snakemake.output_index)
outputs_older_than_script_or_notebook() (snakemake.jobs.Job method)
overall_runtime (snakemake.stats.Stats property)
overwrite_block_content() (snakemake.parser.AbstractCmd method)
overwrite_cmd (snakemake.parser.AbstractCmd attribute)
P
Params (class in snakemake.io)
(class in snakemake.parser)
params (snakemake.jobs.Job property)
(snakemake.rules.Rule property)
(snakemake.rules.RuleProxy property)
params() (snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
params_changed() (snakemake.persistence.Persistence method)
Paramspace (class in snakemake.utils)
,
[1]
parse() (in module snakemake.parser)
parse_batch() (in module snakemake)
parse_config() (in module snakemake)
parse_group_components() (in module snakemake)
parse_groups() (in module snakemake)
parse_key_value_arg() (in module snakemake)
parse_set_ints() (in module snakemake)
parse_set_resources() (in module snakemake)
parse_set_scatter() (in module snakemake)
parse_set_threads() (in module snakemake)
parse_uri() (in module snakemake.common)
patterns (snakemake.io.ReportObject property)
Pepfile (class in snakemake.parser)
Pepschema (class in snakemake.parser)
pepschema() (snakemake.workflow.Workflow method)
PeriodicityDetector (class in snakemake.io)
PeriodicWildcardError
Persistence (class in snakemake.persistence)
pickle_code() (in module snakemake.persistence)
pid (snakemake.benchmark.BenchmarkTimer attribute)
pipe (snakemake.jobs.Reason attribute)
pipe() (in module snakemake.io)
postprocess() (snakemake.dag.DAG method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
PotentialDependency (class in snakemake.dag)
prefix (snakemake.parser.KeywordState attribute)
(snakemake.parser.ModuleKeywordState attribute)
(snakemake.parser.SubworkflowKeywordState attribute)
prefix() (snakemake.shell.shell class method)
prepare() (snakemake.jobs.Job method)
prev_time (snakemake.benchmark.BenchmarkRecord attribute)
print_benchmark_records() (in module snakemake.benchmark)
print_cluster_job_error() (snakemake.executors.ClusterExecutor method)
print_exception() (in module snakemake.exceptions)
print_job_error() (snakemake.executors.AbstractExecutor method)
printcache() (snakemake.executors.DryrunExecutor method)
printjob() (snakemake.executors.AbstractExecutor method)
(snakemake.executors.DryrunExecutor method)
Priority (class in snakemake.parser)
priority (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
priority() (snakemake.dag.DAG method)
(snakemake.workflow.Workflow method)
process (snakemake.executors.SynchronousClusterJob property)
procs (snakemake.benchmark.BenchmarkTimer attribute)
products (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.rules.Rule property)
progress() (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() (snakemake.checkpoints.Checkpoints method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
register_envvars() (snakemake.workflow.Workflow method)
register_job() (snakemake.executors.GenericClusterExecutor method)
(snakemake.executors.RealExecutor method)
register_running() (snakemake.dag.DAG method)
register_secret() (snakemake.executors.KubernetesExecutor method)
register_wildcards() (snakemake.rules.Rule method)
remaining_jobs (snakemake.scheduler.JobScheduler property)
remote() (snakemake.io.Mtime method)
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_output (snakemake.jobs.Job property)
remote_output_newer_than_local (snakemake.jobs.Job property)
remote_output_older_than_local (snakemake.jobs.Job property)
RemoteFileException
remove() (in module snakemake.io)
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)
render_iofile() (in module snakemake.report)
repeat() (in module snakemake.io)
replace_job() (snakemake.dag.DAG method)
Report (class in snakemake.parser)
report() (in module snakemake.io)
(in module snakemake.report)
(in module snakemake.utils)
,
[1]
(snakemake.workflow.Workflow method)
report_job_end() (snakemake.stats.Stats method)
report_job_start() (snakemake.stats.Stats method)
ReportObject (class in snakemake.io)
requested_files() (snakemake.dag.DAG method)
required_by_job() (snakemake.scheduler.JobScheduler method)
reset_params_and_resources() (snakemake.jobs.AbstractJob method)
(snakemake.jobs.GroupJob method)
(snakemake.jobs.Job method)
RESET_SEQ (snakemake.logging.ColorizingStreamHandler attribute)
Resources (class in snakemake.io)
(class in snakemake.parser)
resources (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
resources() (snakemake.workflow.Workflow method)
resources_info() (snakemake.logging.Logger method)
restart_times (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
RMarkdown (class in snakemake.script)
RScript (class in snakemake.script)
Rule (class in snakemake.parser)
(class in snakemake.rules)
rule (snakemake.checkpoints.Checkpoint attribute)
(snakemake.checkpoints.CheckpointJob attribute)
(snakemake.jobs.Job attribute)
rule() (snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
rule2job() (snakemake.dag.DAG method)
rule_dot() (snakemake.dag.DAG method)
rule_dot2() (snakemake.dag.DAG method)
rule_info() (snakemake.logging.Logger method)
rule_prefix() (snakemake.executors.AbstractExecutor method)
rule_stats (snakemake.stats.Stats property)
rule_weight() (snakemake.scheduler.JobScheduler method)
RuleException
RuleKeywordState (class in snakemake.parser)
Ruleorder (class in snakemake.parser)
(class in snakemake.rules)
ruleorder() (snakemake.workflow.Workflow method)
RuleProxy (class in snakemake.rules)
RuleRecord (class in snakemake.report)
Rules (class in snakemake.common)
rules (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
(snakemake.workflow.Workflow property)
Run (class in snakemake.parser)
run() (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_wrapper() (in module snakemake.executors)
running_time (snakemake.benchmark.BenchmarkRecord attribute)
RustScript (class in snakemake.script)
S
S3FileException
safe_delete_pod() (snakemake.executors.KubernetesExecutor method)
Scatter (class in snakemake.common)
Scattergather (class in snakemake.parser)
scattergather() (snakemake.workflow.Workflow method)
schedule() (snakemake.scheduler.JobScheduler method)
ScheduledPeriodicTimer (class in snakemake.benchmark)
Script (class in snakemake.parser)
script() (in module snakemake.script)
(snakemake.workflow.Workflow method)
ScriptBase (class in snakemake.script)
SectionKeywordState (class in snakemake.parser)
SequenceFormatter (class in snakemake.utils)
,
[1]
service (snakemake.jobs.Reason attribute)
service() (in module snakemake.io)
service_info() (snakemake.logging.WMSLogger method)
set_input() (snakemake.rules.Rule method)
set_level() (snakemake.logging.Logger method)
set_log() (snakemake.rules.Rule method)
set_output() (snakemake.rules.Rule method)
set_params() (snakemake.rules.Rule method)
set_pepfile() (snakemake.workflow.Workflow method)
set_stream_handler() (snakemake.logging.Logger method)
set_until_jobs() (snakemake.dag.DAG method)
set_wildcard_constraints() (snakemake.rules.Rule method)
setup_logfile() (snakemake.logging.Logger method)
setup_logger() (in module snakemake.logging)
SFTPFileException
Shadow (class in snakemake.parser)
shadow() (snakemake.workflow.Workflow method)
shadow_dir (snakemake.jobs.Job attribute)
shadowed_path() (snakemake.jobs.Job method)
Shell (class in snakemake.parser)
shell (class in snakemake.shell)
shellcmd (snakemake.jobs.Job property)
shellcmd() (snakemake.logging.Logger method)
(snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
shutdown() (snakemake.executors.AbstractExecutor method)
(snakemake.executors.ClusterExecutor method)
(snakemake.executors.CPUExecutor method)
(snakemake.executors.DRMAAExecutor method)
(snakemake.executors.KubernetesExecutor method)
(snakemake.executors.TibannaExecutor method)
simplify_path() (in module snakemake.utils)
,
[1]
Singularity (class in snakemake.parser)
size (snakemake.io.InputFiles property)
size_mb (snakemake.io.InputFiles property)
SlackLogger (class in snakemake.logging)
sleep() (in module snakemake.executors)
smart_join() (in module snakemake.common)
Snakefile (class in snakemake.parser)
snakefile (snakemake.workflow.Subworkflow property)
(snakemake.workflow.Workflow property)
snakemake
module
Snakemake (class in snakemake.script)
snakemake() (in module snakemake)
,
[1]
snakemake.benchmark
module
snakemake.checkpoints
module
snakemake.common
module
snakemake.cwl
module
snakemake.dag
module
snakemake.decorators
module
snakemake.exceptions
module
snakemake.executors
module
snakemake.io
module
snakemake.jobs
module
snakemake.logging
module
snakemake.output_index
module
snakemake.parser
module
snakemake.persistence
module
snakemake.report
module
snakemake.rules
module
snakemake.scheduler
module
snakemake.script
module
snakemake.shell
module
snakemake.stats
module
snakemake.utils
module
,
[1]
snakemake.workflow
module
snakemake.wrapper
module
source_path() (snakemake.workflow.Workflow method)
SourceFileError
spawn_job() (snakemake.executors.CPUExecutor method)
SpawnedJobError
specialize_rule() (snakemake.dag.DAG method)
split_filename() (snakemake.executors.TibannaExecutor method)
split_git_path() (in module snakemake.io)
srcdir() (in module snakemake.workflow)
start() (snakemake.benchmark.ScheduledPeriodicTimer method)
(snakemake.parser.AbstractCmd method)
(snakemake.parser.Checkpoint method)
(snakemake.parser.DecoratorKeywordState method)
(snakemake.parser.GlobalKeywordState method)
(snakemake.parser.Rule method)
(snakemake.parser.RuleKeywordState method)
(snakemake.parser.Run method)
(snakemake.parser.SectionKeywordState method)
start_func (snakemake.parser.AbstractCmd attribute)
(snakemake.parser.CWL attribute)
(snakemake.parser.Notebook attribute)
(snakemake.parser.Script attribute)
(snakemake.parser.Shell attribute)
(snakemake.parser.TemplateEngine attribute)
(snakemake.parser.Wrapper attribute)
started() (snakemake.persistence.Persistence method)
state_as() (snakemake.parser.UseRule method)
state_from() (snakemake.parser.UseRule method)
state_keyword_rule() (snakemake.parser.UseRule method)
state_modifier() (snakemake.parser.UseRule method)
state_rules_comma_or_end() (snakemake.parser.UseRule method)
state_rules_end() (snakemake.parser.UseRule method)
state_rules_rule() (snakemake.parser.UseRule method)
state_with() (snakemake.parser.UseRule method)
Stats (class in snakemake.stats)
stats (snakemake.scheduler.JobScheduler property)
stats() (snakemake.dag.DAG method)
StopAutomaton
strip_prefix() (in module snakemake.common)
strip_re() (in module snakemake.script)
strip_wildcard_constraints() (in module snakemake.io)
subautomata (snakemake.parser.Module attribute)
(snakemake.parser.Python attribute)
(snakemake.parser.Rule attribute)
(snakemake.parser.Subworkflow attribute)
(snakemake.parser.TokenAutomaton attribute)
(snakemake.parser.UseRule attribute)
subautomaton() (snakemake.parser.TokenAutomaton method)
subcategory (snakemake.io.ReportObject property)
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)
SynchronousClusterExecutor (class in snakemake.executors)
SynchronousClusterJob (class in snakemake.executors)
T
target (snakemake.jobs.Reason attribute)
target() (snakemake.workflow.Subworkflow method)
targetfile (snakemake.jobs.Job attribute)
targets() (snakemake.workflow.Subworkflow method)
TBDString (class in snakemake.common)
temp() (in module snakemake.io)
temp_input() (snakemake.dag.DAG method)
temp_output (snakemake.jobs.Job attribute)
temp_size() (snakemake.dag.DAG method)
template_engine() (snakemake.workflow.Workflow method)
TemplateEngine (class in snakemake.parser)
temporary() (in module snakemake.io)
terminate() (snakemake.shell.shell class method)
TerminatedException
text_handler() (snakemake.logging.Logger method)
Threads (class in snakemake.parser)
threads (snakemake.jobs.GroupJob property)
(snakemake.jobs.Job property)
threads() (snakemake.workflow.Workflow method)
TibannaExecutor (class in snakemake.executors)
TibannaJob (class in snakemake.executors)
tmpdir (snakemake.executors.ClusterExecutor property)
to_json() (snakemake.stats.Stats method)
to_tsv() (snakemake.benchmark.BenchmarkRecord method)
TokenAutomaton (class in snakemake.parser)
toposorted (snakemake.jobs.GroupJob attribute)
toposorted() (snakemake.dag.DAG method)
touch() (in module snakemake.io)
touch_output (snakemake.jobs.Job attribute)
TouchExecutor (class in snakemake.executors)
U
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_incomplete_input_expand_jobs() (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)
UseRule (class in snakemake.parser)
userule() (snakemake.workflow.Workflow method)
uuid() (snakemake.jobs.Job method)
V
validate() (in module snakemake.utils)
,
[1]
Version (class in snakemake.parser)
version (snakemake.rules.Rule property)
version() (snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
version_changed() (snakemake.persistence.Persistence method)
W
wait_for_files() (in module snakemake.io)
warn_about_changes() (snakemake.dag.DAG method)
warning() (snakemake.logging.Logger method)
WebDAVFileException
WHITE (snakemake.logging.ColorizingStreamHandler attribute)
wildcard_constraints (snakemake.rules.Rule property)
wildcard_constraints() (snakemake.workflow.Workflow method)
wildcard_names (snakemake.rules.Rule property)
wildcard_pattern (snakemake.utils.Paramspace property)
,
[1]
WildcardConstraints (class in snakemake.parser)
WildcardError
Wildcards (class in snakemake.io)
wildcards (snakemake.jobs.Job attribute)
wildcards_dict (snakemake.jobs.Job attribute)
win_command_prefix() (snakemake.shell.shell class method)
WMSLogger (class in snakemake.logging)
work() (snakemake.benchmark.BenchmarkTimer method)
(snakemake.benchmark.ScheduledPeriodicTimer method)
Workdir (class in snakemake.parser)
workdir (snakemake.workflow.Subworkflow property)
workdir() (snakemake.workflow.Workflow method)
Workflow (class in snakemake.workflow)
WorkflowError
Wrapper (class in snakemake.parser)
wrapper() (in module snakemake.wrapper)
(snakemake.workflow.Workflow method)
write_benchmark_records() (in module snakemake.benchmark)
write_jobscript() (snakemake.executors.ClusterExecutor method)
write_script() (snakemake.script.JuliaScript method)
(snakemake.script.PythonScript method)
(snakemake.script.RMarkdown method)
(snakemake.script.RScript method)
(snakemake.script.RustScript method)
(snakemake.script.ScriptBase method)
X
XRootDFileException
Y
YELLOW (snakemake.logging.ColorizingStreamHandler attribute)
yield_indent() (snakemake.parser.KeywordState method)
Z
ZenodoFileException
Read the Docs
v: v7.2.1
Versions
master
latest
stable
v7.2.1
v7.2.0
v7.1.1
v7.1.0
v7.0.4
v7.0.3
v7.0.2
v7.0.1
v7.0.0
v6.15.5
v6.15.4
v6.15.3
v6.15.2
v6.15.1
v6.15.0
v6.14.0
v6.13.1
v6.13.0
v6.12.3
v6.12.2
v6.12.1
v6.12.0
v6.11.1
v6.11.0
v6.10.0
v6.9.1
v6.9.0
v6.8.2
v6.8.1
v6.8.0
v6.7.0
v6.6.1
v6.6.0
v6.5.5
v6.5.4
v6.5.3
v6.5.2
v6.5.1
v6.5.0
v6.4.1
v6.4.0
v6.3.0
v6.2.1
v6.2.0
v6.1.2
v6.1.1
v6.1.0
v6.0.5
v6.0.4
v6.0.3
v6.0.2
v6.0.1
v6.0.0
v5.32.2
v5.32.1
v5.32.0
v5.31.1
v5.31.0
v5.30.2
v5.30.1
v5.30.0
v5.29.0
v5.28.0
v5.27.4
v5.27.3
v5.27.2
v5.27.1
v5.27.0
v5.26.1
v5.26.0
v5.25.0
v5.24.2
v5.24.1
v5.24.0
v5.23.0
v5.22.1
v5.22.0
v5.21.0
v5.20.1
v5.20.0
v5.19.3
v5.19.2
v5.19.1
v5.19.0
v5.18.1
v5.18.0
v5.17.0
v5.16.0
v5.15.0
v5.14.0
v5.13.0
v5.12.3
v5.12.2
v5.12.1
v5.12.0
v5.11.2
v5.11.1
v5.11.0
v5.10.0
v5.9.1
v5.9.0
v5.8.2
v5.8.1
v5.8.0
v5.7.4
v5.7.3
v5.7.2
v5.7.1
v5.7.0
v5.6.0
v5.5.4
v5.5.3
v5.5.2
v5.5.1
v5.5.0
v5.4.5
v5.4.4
v5.4.3
v5.4.2
v5.4.1
v5.4.0
v5.3.1
v5.3.0
v5.2.4
v5.2.3
v5.2.2
v5.2.1
v5.2.0
v5.1.5
v5.1.4
v5.1.3
v5.1.2
v5.1.1
v5.0.0
v4.8.1
v4.8.0
v4.7.0
v4.6.0
v4.5.1
v4.5.0
v4.3.0
v4.2.0
v4.1.0
v4.0.0
v3.13.3
v3.13.2
v3.13.1
v3.13.0
v3.12.0
v3.11.2
v3.11.1
v3.11.0
v3.10.2
v3.10.1
v3.10.0
v3.9.1
v3.9.0
v3.7.1
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.