Snakemake
5.7.4
Getting started
Installation
Examples
Snakemake Tutorial
Short tutorial
Executing workflows
Executing Snakemake
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 attribute)
add() (snakemake.report.RuleRecord method)
(snakemake.rules.Ruleorder method)
add_command() (snakemake.executors.TibannaExecutor method)
add_name() (snakemake.io.Namedlist 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 attribute)
allitems() (snakemake.io.Namedlist method)
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)
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)
archive_file (snakemake.conda.Env attribute)
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.Script method)
(snakemake.parser.Shell method)
(snakemake.parser.Wrapper method)
argvquote() (in module snakemake.utils)
,
[1]
attempt (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
auto_report() (in module snakemake.report)
available_cpu_count() (in module snakemake.utils)
,
[1]
available_protocols (snakemake.remote.dropbox.RemoteProvider attribute)
(snakemake.remote.EGA.RemoteProvider attribute)
(snakemake.remote.HTTP.RemoteProvider attribute)
(snakemake.remote.NCBI.RemoteProvider attribute)
(snakemake.remote.S3.RemoteProvider attribute)
available_protocols() (snakemake.remote.AbstractRemoteProvider method)
AzureFileException
B
b64id (snakemake.jobs.Job attribute)
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 attribute)
(snakemake.rules.Rule attribute)
(snakemake.rules.RuleProxy attribute)
benchmark() (snakemake.workflow.Workflow method)
BENCHMARK_INTERVAL (in module snakemake.benchmark)
BENCHMARK_INTERVAL_SHORT (in module snakemake.benchmark)
benchmark_repeats (snakemake.jobs.Job attribute)
benchmarked() (in module snakemake.benchmark)
BenchmarkRecord (class in snakemake.benchmark)
BenchmarkTimer (class in snakemake.benchmark)
bfs() (snakemake.dag.DAG method)
bin_path() (snakemake.conda.Conda 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)
C
cache_job() (snakemake.dag.DAG method)
cached (snakemake.common.lazy_property attribute)
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.CPUExecutor method)
(snakemake.executors.ClusterExecutor 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_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_wildcards() (snakemake.rules.Rule method)
Checkpoint (class in snakemake.checkpoints)
(class in snakemake.parser)
checkpoint_jobs (snakemake.dag.DAG attribute)
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)
ChildIOException
clean() (snakemake.common.lazy_property static method)
(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_conda() (snakemake.persistence.Persistence method)
cleanup_locks() (snakemake.persistence.Persistence method)
cleanup_metadata() (snakemake.persistence.Persistence method)
cleanup_shadow() (snakemake.persistence.Persistence method)
clear() (snakemake.io.IOCache method)
clone() (snakemake.io.Namedlist 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 attribute)
Conda (class in snakemake.conda)
(class in snakemake.parser)
conda() (snakemake.workflow.Workflow method)
conda_env (snakemake.jobs.Job attribute)
(snakemake.rules.Rule attribute)
conda_env_file (snakemake.jobs.Job attribute)
conda_env_path (snakemake.jobs.Job attribute)
config (snakemake.workflow.Workflow attribute)
Configfile (class in snakemake.parser)
configfile() (snakemake.workflow.Workflow method)
ConfigfileRecord (class in snakemake.report)
consume() (snakemake.parser.TokenAutomaton method)
contains_wildcard() (in module snakemake.io)
contains_wildcard_constraints() (in module snakemake.io)
content (snakemake.conda.Env attribute)
content() (in module snakemake.conda)
content_hash (snakemake.conda.Env attribute)
cpu_seconds (snakemake.benchmark.BenchmarkRecord attribute)
CPUExecutor (class in snakemake.executors)
create() (snakemake.conda.Env method)
create_archive() (snakemake.conda.Env method)
create_conda_envs() (snakemake.dag.DAG method)
CreateCondaEnvironmentException
CreateRuleException
cumsum() (in module snakemake.scheduler)
current_basedir (snakemake.workflow.Workflow attribute)
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 attribute)
(snakemake.jobs.Job attribute)
dag() (in module snakemake.gui)
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 attribute)
(snakemake.parser.TokenAutomaton attribute)
default (snakemake.common.Mode attribute)
default_jobscript (snakemake.executors.ClusterExecutor attribute)
default_protocol (snakemake.remote.dropbox.RemoteProvider attribute)
(snakemake.remote.EGA.RemoteProvider attribute)
(snakemake.remote.HTTP.RemoteProvider attribute)
(snakemake.remote.NCBI.RemoteProvider attribute)
(snakemake.remote.S3.RemoteProvider attribute)
default_protocol() (snakemake.remote.AbstractRemoteProvider method)
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.EGA.RemoteObject method)
(snakemake.remote.HTTP.RemoteObject method)
(snakemake.remote.NCBI.RemoteObject method)
(snakemake.remote.S3.RemoteObject method)
(snakemake.remote.dropbox.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.GroupJob attribute)
(snakemake.jobs.Job attribute)
dynamic_output (snakemake.jobs.Job attribute)
dynamic_output_jobs (snakemake.dag.DAG attribute)
dynamic_wildcards (snakemake.jobs.Job attribute)
E
effective_indent (snakemake.parser.TokenAutomaton attribute)
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)
empty_remote_dirs (snakemake.jobs.Job attribute)
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.Script attribute)
(snakemake.parser.Shell attribute)
(snakemake.parser.Wrapper attribute)
Env (class in snakemake.conda)
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)
escape_backslash() (in module snakemake.common)
exec_arn (snakemake.executors.TibannaJob attribute)
executable() (snakemake.shell.shell class method)
execute() (snakemake.workflow.Workflow method)
existing_output (snakemake.jobs.Job attribute)
existing_remote_input (snakemake.jobs.Job attribute)
existing_remote_output (snakemake.jobs.Job attribute)
exists() (snakemake.remote.AbstractRemoteObject 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)
(snakemake.remote.dropbox.RemoteObject method)
exists_in_bucket() (snakemake.remote.S3.S3Helper method)
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 attribute)
(snakemake.jobs.Job attribute)
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 attribute)
file_stats (snakemake.stats.Stats attribute)
filegraph_dot() (snakemake.dag.DAG method)
FileRecord (class in snakemake.report)
files (snakemake.persistence.Persistence attribute)
files_to_download (snakemake.jobs.Job attribute)
files_to_upload (snakemake.jobs.Job attribute)
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 attribute)
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)
(in module snakemake.workflow)
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
GenericClusterExecutor (class in snakemake.executors)
GenericClusterJob (class in snakemake.executors)
get() (snakemake.checkpoints.Checkpoint method)
(snakemake.io.Namedlist 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_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_jobs_or_groups() (snakemake.dag.DAG method)
get_jobscript() (snakemake.executors.ClusterExecutor method)
get_last_stable_version() (in module snakemake.common)
get_logfile() (snakemake.logging.Logger method)
get_names() (snakemake.io.Namedlist method)
get_path() (in module snakemake.wrapper)
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_singularity_envvars() (snakemake.conda.Env class 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)
(snakemake.remote.AbstractRemoteProvider method)
global_singularity() (snakemake.workflow.Workflow method)
global_wildcard_constraints() (snakemake.workflow.Workflow method)
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 attribute)
group() (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)
guess_db_options_for_extension() (snakemake.remote.NCBI.NCBIHelper method)
H
handle_job_error() (snakemake.executors.AbstractExecutor method)
(snakemake.executors.CPUExecutor method)
(snakemake.executors.ClusterExecutor method)
(snakemake.executors.RealExecutor method)
handle_job_success() (snakemake.executors.AbstractExecutor method)
(snakemake.executors.CPUExecutor method)
(snakemake.executors.ClusterExecutor 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)
hash (snakemake.conda.Env attribute)
(snakemake.singularity.Image attribute)
HIGHEST_PRIORITY (snakemake.jobs.Job attribute)
host (snakemake.remote.DomainObject attribute)
HTTPFileException
httpr() (snakemake.remote.HTTP.RemoteObject method)
I
icon (snakemake.report.FileRecord attribute)
id (snakemake.remote.EGA.EGAFileInfo attribute)
Image (class in snakemake.singularity)
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 attribute)
incomplete_output (snakemake.jobs.Reason attribute)
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.GroupJob attribute)
(snakemake.jobs.Job attribute)
(snakemake.rules.Rule attribute)
(snakemake.rules.RuleProxy attribute)
input() (snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
input_changed() (snakemake.persistence.Persistence method)
input_maxtime (snakemake.jobs.Job attribute)
InputFiles (class in snakemake.io)
InputFunctionException
inputsize (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
insert_items() (snakemake.io.Namedlist method)
instances (snakemake.conda.Conda attribute)
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 attribute)
(snakemake.jobs.Job attribute)
is_callable() (in module snakemake.io)
is_checkpoint (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
is_colon() (in module snakemake.parser)
is_comma() (in module snakemake.parser)
is_comment() (in module snakemake.parser)
is_cwl (snakemake.jobs.Job attribute)
is_dedent() (in module snakemake.parser)
is_eof() (in module snakemake.parser)
is_final (snakemake.dag.Batch attribute)
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 attribute)
is_indent() (in module snakemake.parser)
is_local (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
(snakemake.singularity.Image attribute)
is_local() (in module snakemake.wrapper)
(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 attribute)
is_op() (in module snakemake.parser)
is_periodic() (snakemake.io.PeriodicityDetector method)
is_producer() (snakemake.rules.Rule method)
is_rule() (snakemake.workflow.Workflow method)
is_run (snakemake.jobs.Job attribute)
is_script (snakemake.jobs.Job attribute)
is_script() (in module snakemake.wrapper)
is_shadow (snakemake.jobs.Job attribute)
is_shell (snakemake.jobs.Job attribute)
is_string() (in module snakemake.parser)
is_table (snakemake.report.FileRecord attribute)
is_text (snakemake.report.FileRecord attribute)
is_tty (snakemake.logging.ColorizingStreamHandler attribute)
is_updated (snakemake.jobs.GroupJob attribute)
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 attribute)
is_wrapper (snakemake.jobs.Job attribute)
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)
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)
(snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
jobid() (snakemake.dag.DAG method)
jobname (snakemake.executors.TibannaJob attribute)
JobRecord (class in snakemake.report)
jobs (snakemake.dag.DAG attribute)
(snakemake.jobs.GroupJob attribute)
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)
K
key_last_modified() (snakemake.remote.S3.S3Helper method)
key_size() (snakemake.remote.S3.S3Helper method)
keys() (snakemake.io.Namedlist method)
keyword (snakemake.parser.GlobalSingularity attribute)
(snakemake.parser.GlobalWildcardConstraints attribute)
(snakemake.parser.KeywordState attribute)
(snakemake.parser.WildcardConstraints attribute)
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
lazy_property (class in snakemake.common)
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)
list (snakemake.remote.dropbox.RemoteObject attribute)
(snakemake.remote.HTTP.RemoteObject attribute)
(snakemake.remote.NCBI.RemoteObject attribute)
(snakemake.remote.S3.RemoteObject attribute)
list() (snakemake.remote.AbstractRemoteObject method)
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 attribute)
local_needrun_jobs (snakemake.dag.DAG attribute)
local_output (snakemake.jobs.Job attribute)
local_path (snakemake.remote.DomainObject attribute)
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 attribute)
Log (class in snakemake.io)
(class in snakemake.parser)
log (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
(snakemake.rules.Rule attribute)
(snakemake.rules.RuleProxy attribute)
log() (in module snakemake.gui)
(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_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 attribute)
message() (snakemake.workflow.Workflow method)
messages (snakemake.exceptions.RuleException attribute)
metadata() (snakemake.persistence.Persistence method)
method (snakemake.common.lazy_property attribute)
mime_from_file() (in module snakemake.report)
min_version() (in module snakemake.utils)
,
[1]
missing_input (snakemake.jobs.Job attribute)
missing_output (snakemake.jobs.Reason attribute)
missing_output() (snakemake.jobs.Job method)
missing_remote_input (snakemake.jobs.Job attribute)
missing_remote_output (snakemake.jobs.Job attribute)
missing_temp() (snakemake.dag.DAG method)
MissingInputException
MissingOutputException
MissingRuleException
Mode (class in snakemake.common)
mtime() (snakemake.remote.AbstractRemoteObject 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)
(snakemake.remote.dropbox.RemoteObject method)
N
name (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
(snakemake.remote.DomainObject attribute)
(snakemake.remote.S3.RemoteObject attribute)
(snakemake.remote.dropbox.RemoteObject attribute)
(snakemake.report.FileRecord attribute)
name() (snakemake.parser.Rule method)
(snakemake.parser.Subworkflow method)
(snakemake.remote.AbstractRemoteObject method)
Namedlist (class in snakemake.io)
NCBIFileException
NCBIHelper (class in snakemake.remote.NCBI)
needrun() (snakemake.dag.DAG method)
needrun_jobs (snakemake.dag.DAG attribute)
needs_singularity (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
new_job() (snakemake.dag.DAG method)
new_wildcards() (snakemake.dag.DAG method)
newversion_files (snakemake.dag.DAG attribute)
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)
num_if_possible() (in module snakemake.common)
O
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 attribute)
options_for_db_and_extension() (snakemake.remote.NCBI.NCBIHelper method)
Output (class in snakemake.parser)
output (snakemake.checkpoints.CheckpointJob attribute)
(snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
(snakemake.rules.Rule attribute)
(snakemake.rules.RuleProxy attribute)
output() (snakemake.workflow.Workflow method)
output_mintime (snakemake.jobs.Job attribute)
output_mintime_local (snakemake.jobs.Job attribute)
OutputFiles (class in snakemake.io)
OutputIndex (class in snakemake.output_index)
outputs_older_than_script() (snakemake.jobs.Job method)
overall_runtime (snakemake.stats.Stats attribute)
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 attribute)
(snakemake.rules.Rule attribute)
(snakemake.rules.RuleProxy attribute)
params() (snakemake.persistence.Persistence method)
(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)
parts (snakemake.remote.EGA.RemoteObject attribute)
path (snakemake.conda.Env attribute)
(snakemake.remote.EGA.EGAFile attribute)
(snakemake.singularity.Image attribute)
path_prefix (snakemake.remote.DomainObject attribute)
path_remainder (snakemake.remote.DomainObject attribute)
PeriodicityDetector (class in snakemake.io)
PeriodicWildcardError
Persistence (class in snakemake.persistence)
pickle_code() (in module snakemake.persistence)
pid (snakemake.benchmark.BenchmarkTimer attribute)
pipe() (in module snakemake.io)
plainstrings() (snakemake.io.Namedlist method)
port (snakemake.remote.DomainObject attribute)
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)
prefix_path() (snakemake.conda.Conda 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)
printjob() (snakemake.executors.AbstractExecutor method)
Priority (class in snakemake.parser)
priority (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
priority() (snakemake.dag.DAG method)
(snakemake.workflow.Workflow method)
process (snakemake.executors.SynchronousClusterJob attribute)
procs (snakemake.benchmark.BenchmarkTimer attribute)
products (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
(snakemake.rules.Rule attribute)
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() (snakemake.singularity.Image method)
pull_singularity_imgs() (snakemake.dag.DAG method)
Python (class in snakemake.parser)
python() (snakemake.parser.Python method)
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 attribute)
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_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 attribute)
remote_input_newer_than_local (snakemake.jobs.Job attribute)
remote_input_older_than_local (snakemake.jobs.Job attribute)
remote_interface() (snakemake.remote.AbstractRemoteProvider method)
(snakemake.remote.NCBI.RemoteProvider method)
(snakemake.remote.S3.RemoteProvider method)
(snakemake.remote.dropbox.RemoteProvider method)
remote_output (snakemake.jobs.Job attribute)
remote_output_newer_than_local (snakemake.jobs.Job attribute)
remote_output_older_than_local (snakemake.jobs.Job attribute)
remote_path (snakemake.remote.DomainObject attribute)
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 attribute)
(snakemake.jobs.Job attribute)
resources() (snakemake.workflow.Workflow method)
resources_info() (snakemake.logging.Logger method)
restart_times (snakemake.jobs.GroupJob attribute)
(snakemake.jobs.Job attribute)
rmdir_empty_remote_dirs() (snakemake.jobs.Job method)
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 attribute)
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 attribute)
(snakemake.jobs.Job attribute)
(snakemake.workflow.Workflow attribute)
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_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 attribute)
s3_create_stub() (snakemake.remote.S3.RemoteObject method)
s3_key (snakemake.remote.S3.RemoteObject attribute)
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)
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_name() (snakemake.io.Namedlist 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 attribute)
shellcmd() (in module snakemake.singularity)
(snakemake.conda.Conda method)
(snakemake.logging.Logger method)
(snakemake.persistence.Persistence method)
(snakemake.workflow.Workflow method)
shutdown() (snakemake.executors.AbstractExecutor method)
(snakemake.executors.CPUExecutor method)
(snakemake.executors.ClusterExecutor 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)
singularity() (snakemake.workflow.Workflow method)
singularity_img (snakemake.jobs.Job attribute)
(snakemake.rules.Rule attribute)
singularity_img_path (snakemake.jobs.Job attribute)
singularity_img_url (snakemake.conda.Env attribute)
(snakemake.jobs.Job attribute)
size (snakemake.io.InputFiles attribute)
(snakemake.remote.EGA.EGAFileInfo attribute)
size() (snakemake.remote.AbstractRemoteObject 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.dropbox.RemoteObject method)
sleep() (in module snakemake.executors)
Snakefile (class in snakemake.parser)
snakefile (snakemake.workflow.Subworkflow attribute)
Snakemake (class in snakemake.script)
snakemake (module)
snakemake() (in module snakemake)
,
[1]
snakemake.benchmark (module)
snakemake.checkpoints (module)
snakemake.common (module)
snakemake.conda (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.singularity (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.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.scheduler.JobScheduler attribute)
stats() (snakemake.dag.DAG method)
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)
stripped_constraints() (snakemake.io.Namedlist method)
subautomata (snakemake.parser.Python attribute)
(snakemake.parser.Rule attribute)
(snakemake.parser.Subworkflow attribute)
(snakemake.parser.TokenAutomaton attribute)
subautomaton() (snakemake.parser.TokenAutomaton method)
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 attribute)
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
take_names() (snakemake.io.Namedlist method)
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 attribute)
(snakemake.jobs.Job attribute)
threads() (snakemake.workflow.Workflow method)
TibannaExecutor (class in snakemake.executors)
TibannaJob (class in snakemake.executors)
tmpdir (snakemake.executors.ClusterExecutor attribute)
to_json() (snakemake.stats.Stats method)
to_tsv() (snakemake.benchmark.BenchmarkRecord method)
token (snakemake.remote.EGA.RemoteProvider attribute)
TokenAutomaton (class in snakemake.parser)
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 attribute)
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 attribute)
updated_input_run (snakemake.jobs.Reason attribute)
upload() (snakemake.remote.AbstractRemoteObject method)
(snakemake.remote.HTTP.RemoteObject method)
(snakemake.remote.NCBI.RemoteObject method)
(snakemake.remote.S3.RemoteObject method)
(snakemake.remote.dropbox.RemoteObject method)
upload_to_s3() (snakemake.remote.S3.S3Helper method)
V
valid_dbs (snakemake.remote.NCBI.NCBIHelper attribute)
valid_extensions (snakemake.remote.NCBI.NCBIHelper attribute)
validate() (in module snakemake.utils)
,
[1]
Version (class in snakemake.parser)
version (snakemake.remote.NCBI.RemoteObject attribute)
(snakemake.rules.Rule attribute)
version() (snakemake.persistence.Persistence method)
(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 attribute)
wildcard_constraints() (snakemake.workflow.Workflow method)
wildcard_names (snakemake.rules.Rule attribute)
WildcardConstraints (class in snakemake.parser)
WildcardError
Wildcards (class in snakemake.io)
wildcards (snakemake.jobs.Job attribute)
wildcards_dict (snakemake.jobs.Job attribute)
work() (snakemake.benchmark.BenchmarkTimer method)
(snakemake.benchmark.ScheduledPeriodicTimer method)
Workdir (class in snakemake.parser)
workdir (snakemake.workflow.Subworkflow attribute)
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)
X
XRootDFileException
Y
YELLOW (snakemake.logging.ColorizingStreamHandler attribute)
yield_indent() (snakemake.parser.KeywordState method)