Snakemake
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Getting started
安装
示例
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
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A
AbstractCmd (snakemake.parser 中的类)
AbstractExecutor (snakemake.executors 中的类)
AbstractJob (snakemake.jobs 中的类)
AbstractRemoteObject (snakemake.remote 中的类)
AbstractRemoteProvider (snakemake.remote 中的类)
add() (snakemake.report.RuleRecord 方法)
(snakemake.rules.Ruleorder 方法)
add_name() (snakemake.io.Namedlist 方法)
add_rule() (snakemake.workflow.Workflow 方法)
all_inputfiles() (snakemake.persistence.Persistence 方法)
all_outputfiles() (snakemake.persistence.Persistence 方法)
all_products (snakemake.jobs.GroupJob 属性)
allitems() (snakemake.io.Namedlist 方法)
allows_directories (snakemake.remote.AbstractRemoteProvider 属性)
(snakemake.remote.FTP.RemoteProvider 属性)
(snakemake.remote.SFTP.RemoteProvider 属性)
AlwaysQuotedFormatter (snakemake.utils 中的类)
,
[1]
AmbiguousRuleException
ancient() (在 snakemake.io 模块中)
AnnotatedString (snakemake.io 中的类)
api_request() (snakemake.remote.EGA.RemoteProvider 方法)
apply_default_remote() (snakemake.rules.Rule 方法)
apply_input_function() (snakemake.rules.Rule 方法)
apply_wildcards() (在 snakemake.io 模块中)
archive() (snakemake.dag.DAG 方法)
archive_conda_env() (snakemake.jobs.Job 方法)
archive_file (snakemake.conda.Env 属性)
args (snakemake.parser.DecoratorKeywordState 属性)
(snakemake.parser.OnError 属性)
(snakemake.parser.OnStart 属性)
(snakemake.parser.OnSuccess 属性)
args() (snakemake.parser.AbstractCmd 方法)
(snakemake.parser.CWL 方法)
(snakemake.parser.Script 方法)
(snakemake.parser.Shell 方法)
(snakemake.parser.Wrapper 方法)
argvquote() (在 snakemake.utils 模块中)
,
[1]
attempt (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
auto_report() (在 snakemake.report 模块中)
available_cpu_count() (在 snakemake.utils 模块中)
,
[1]
available_protocols (snakemake.remote.dropbox.RemoteProvider 属性)
(snakemake.remote.EGA.RemoteProvider 属性)
(snakemake.remote.FTP.RemoteProvider 属性)
(snakemake.remote.HTTP.RemoteProvider 属性)
(snakemake.remote.S3.RemoteProvider 属性)
(snakemake.remote.SFTP.RemoteProvider 属性)
(snakemake.remote.webdav.RemoteProvider 属性)
available_protocols() (snakemake.remote.AbstractRemoteProvider 方法)
B
b64id (snakemake.jobs.Job 属性)
bash_completion() (在 snakemake 模块中)
bench_record (snakemake.benchmark.BenchmarkTimer 属性)
benchmark (snakemake.jobs.Job 属性)
Benchmark (snakemake.parser 中的类)
benchmark (snakemake.rules.Rule 属性)
(snakemake.rules.RuleProxy 属性)
benchmark() (snakemake.workflow.Workflow 方法)
BENCHMARK_INTERVAL() (在 snakemake.benchmark 模块中)
BENCHMARK_INTERVAL_SHORT() (在 snakemake.benchmark 模块中)
benchmark_repeats (snakemake.jobs.Job 属性)
benchmarked() (在 snakemake.benchmark 模块中)
BenchmarkRecord (snakemake.benchmark 中的类)
BenchmarkTimer (snakemake.benchmark 中的类)
bfs() (snakemake.dag.DAG 方法)
bin_path() (snakemake.conda.Conda 方法)
BLACK (snakemake.logging.ColorizingStreamHandler 属性)
block() (snakemake.parser.KeywordState 方法)
block_content() (snakemake.parser.AbstractCmd 方法)
(snakemake.parser.KeywordState 方法)
(snakemake.parser.Localrules 方法)
(snakemake.parser.Rule 方法)
(snakemake.parser.Ruleorder 方法)
(snakemake.parser.Run 方法)
(snakemake.parser.Subworkflow 方法)
BLUE (snakemake.logging.ColorizingStreamHandler 属性)
BOLD_SEQ (snakemake.logging.ColorizingStreamHandler 属性)
bucket_exists() (snakemake.remote.S3.S3Helper 方法)
C
cached (snakemake.common.lazy_property 属性)
calc_resource() (snakemake.scheduler.JobScheduler 方法)
callback (snakemake.executors.DRMAAClusterJob 属性)
(snakemake.executors.GenericClusterJob 属性)
(snakemake.executors.KubernetesJob 属性)
(snakemake.executors.SynchronousClusterJob 属性)
can_color_tty() (snakemake.logging.ColorizingStreamHandler 方法)
cancel() (snakemake.benchmark.DaemonTimer 方法)
(snakemake.benchmark.ScheduledPeriodicTimer 方法)
(snakemake.executors.AbstractExecutor 方法)
(snakemake.executors.CPUExecutor 方法)
(snakemake.executors.ClusterExecutor 方法)
(snakemake.executors.DRMAAExecutor 方法)
(snakemake.executors.GenericClusterExecutor 方法)
(snakemake.executors.KubernetesExecutor 方法)
(snakemake.executors.SynchronousClusterExecutor 方法)
candidate() (snakemake.scheduler.JobScheduler 方法)
caption (snakemake.io.ReportObject 属性)
category (snakemake.io.ReportObject 属性)
Category (snakemake.report 中的类)
change_working_directory() (在 snakemake.executors 模块中)
check() (snakemake.workflow.Workflow 方法)
check_and_touch_output() (snakemake.dag.DAG 方法)
check_dynamic() (snakemake.dag.DAG 方法)
check_incomplete() (snakemake.dag.DAG 方法)
check_localrules() (snakemake.workflow.Workflow 方法)
check_output() (snakemake.shell.shell 类方法)
check_output_duplicates() (snakemake.rules.Rule 方法)
check_periodic_wildcards() (snakemake.dag.DAG 方法)
check_protected_output() (snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
check_wildcards() (snakemake.rules.Rule 方法)
Checkpoint (snakemake.checkpoints 中的类)
(snakemake.parser 中的类)
checkpoint_jobs (snakemake.dag.DAG 属性)
checkpoint_target() (在 snakemake.io 模块中)
CheckpointJob (snakemake.checkpoints 中的类)
Checkpoints (snakemake.checkpoints 中的类)
checkpoints (snakemake.checkpoints.Checkpoint 属性)
checksum (snakemake.remote.EGA.EGAFileInfo 属性)
ChildIOException
clean() (snakemake.common.lazy_property 静态方法)
(snakemake.dag.DAG 方法)
cleanup() (snakemake.dag.DAG 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
(snakemake.logging.Logger 方法)
(snakemake.persistence.Persistence 方法)
(snakemake.shell.shell 类方法)
cleanup_conda() (snakemake.persistence.Persistence 方法)
cleanup_locks() (snakemake.persistence.Persistence 方法)
cleanup_metadata() (snakemake.persistence.Persistence 方法)
cleanup_shadow() (snakemake.persistence.Persistence 方法)
clear() (snakemake.io.IOCache 方法)
clone() (snakemake.io.Namedlist 方法)
close() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.FTP.RemoteObject 方法)
close_remote() (snakemake.jobs.Job 方法)
close_remote_objects() (snakemake.dag.DAG 方法)
cluster (snakemake.common.Mode 属性)
cluster_params() (snakemake.executors.ClusterExecutor 方法)
cluster_wildcards() (snakemake.executors.ClusterExecutor 方法)
ClusterExecutor (snakemake.executors 中的类)
ClusterJobException
code() (snakemake.persistence.Persistence 方法)
(snakemake.report.ConfigfileRecord 方法)
(snakemake.report.RuleRecord 方法)
code_changed() (snakemake.persistence.Persistence 方法)
collect_potential_dependencies() (snakemake.dag.DAG 方法)
colon() (snakemake.parser.KeywordState 方法)
COLOR_SEQ (snakemake.logging.ColorizingStreamHandler 属性)
ColorizingStreamHandler (snakemake.logging 中的类)
colors (snakemake.logging.ColorizingStreamHandler 属性)
compare() (snakemake.rules.Ruleorder 方法)
concrete_files (snakemake.workflow.Workflow 属性)
Conda (snakemake.conda 中的类)
(snakemake.parser 中的类)
conda() (snakemake.workflow.Workflow 方法)
conda_env (snakemake.jobs.Job 属性)
(snakemake.rules.Rule 属性)
conda_env_file (snakemake.jobs.Job 属性)
conda_env_path (snakemake.jobs.Job 属性)
config (snakemake.workflow.Workflow 属性)
Configfile (snakemake.parser 中的类)
configfile() (snakemake.workflow.Workflow 方法)
ConfigfileRecord (snakemake.report 中的类)
consume() (snakemake.parser.TokenAutomaton 方法)
contains_wildcard() (在 snakemake.io 模块中)
contains_wildcard_constraints() (在 snakemake.io 模块中)
content (snakemake.conda.Env 属性)
content() (在 snakemake.conda 模块中)
content_hash (snakemake.conda.Env 属性)
cpu_seconds (snakemake.benchmark.BenchmarkRecord 属性)
CPUExecutor (snakemake.executors 中的类)
create() (snakemake.conda.Env 方法)
create_archive() (snakemake.conda.Env 方法)
create_conda_envs() (snakemake.dag.DAG 方法)
CreateCondaEnvironmentException
CreateRuleException
cumsum() (在 snakemake.scheduler 模块中)
current_basedir (snakemake.workflow.Workflow 属性)
cut_traceback() (在 snakemake.exceptions 模块中)
CWL (snakemake.parser 中的类)
cwl() (snakemake.workflow.Workflow 方法)
(在 snakemake.cwl 模块中)
CYAN (snakemake.logging.ColorizingStreamHandler 属性)
CyclicGraphException
D
d3dag() (snakemake.dag.DAG 方法)
(snakemake.logging.Logger 方法)
DaemonTimer (snakemake.benchmark 中的类)
DAG (snakemake.dag 中的类)
dag (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
dag() (在 snakemake.gui 模块中)
dag_debug() (snakemake.logging.Logger 方法)
dag_to_cwl() (在 snakemake.cwl 模块中)
data_uri() (在 snakemake.report 模块中)
data_uri_from_file() (在 snakemake.report 模块中)
dataset (snakemake.remote.EGA.EGAFile 属性)
deactivate() (snakemake.io.IOCache 方法)
deactivate_cache() (snakemake.persistence.Persistence 方法)
debug() (snakemake.logging.Logger 方法)
dec_all_methods() (在 snakemake.decorators 模块中)
decorate() (snakemake.logging.ColorizingStreamHandler 方法)
decorate_end() (snakemake.parser.AbstractCmd 方法)
(snakemake.parser.KeywordState 方法)
decorator (snakemake.parser.DecoratorKeywordState 属性)
(snakemake.parser.OnError 属性)
(snakemake.parser.OnStart 属性)
(snakemake.parser.OnSuccess 属性)
DecoratorKeywordState (snakemake.parser 中的类)
dedent (snakemake.parser.Rule 属性)
(snakemake.parser.TokenAutomaton 属性)
default (snakemake.common.Mode 属性)
default_jobscript (snakemake.executors.ClusterExecutor 属性)
default_protocol (snakemake.remote.dropbox.RemoteProvider 属性)
(snakemake.remote.EGA.RemoteProvider 属性)
(snakemake.remote.FTP.RemoteProvider 属性)
(snakemake.remote.HTTP.RemoteProvider 属性)
(snakemake.remote.S3.RemoteProvider 属性)
(snakemake.remote.SFTP.RemoteProvider 属性)
(snakemake.remote.webdav.RemoteProvider 属性)
default_protocol() (snakemake.remote.AbstractRemoteProvider 方法)
delete_from_bucket() (snakemake.remote.S3.S3Helper 方法)
delete_job() (snakemake.dag.DAG 方法)
delete_omitfrom_jobs() (snakemake.dag.DAG 方法)
dependencies (snakemake.jobs.Job 属性)
derived (snakemake.jobs.Reason 属性)
dfs() (snakemake.dag.DAG 方法)
directory() (在 snakemake.io 模块中)
docstring() (snakemake.workflow.Workflow 方法)
DomainObject (snakemake.remote 中的类)
dot() (snakemake.dag.DAG 方法)
download() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.EGA.RemoteObject 方法)
(snakemake.remote.FTP.RemoteObject 方法)
(snakemake.remote.HTTP.RemoteObject 方法)
(snakemake.remote.S3.RemoteObject 方法)
(snakemake.remote.SFTP.RemoteObject 方法)
(snakemake.remote.dropbox.RemoteObject 方法)
(snakemake.remote.webdav.RemoteObject 方法)
download_from_s3() (snakemake.remote.S3.S3Helper 方法)
download_remote_input() (snakemake.jobs.AbstractJob 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
downstream_of_omitfrom() (snakemake.dag.DAG 方法)
DRMAAClusterJob (snakemake.executors 中的类)
DRMAAExecutor (snakemake.executors 中的类)
dropbox_file() (snakemake.remote.dropbox.RemoteObject 方法)
DropboxFileException
dryrun() (在 snakemake.gui 模块中)
DryrunExecutor (snakemake.executors 中的类)
DummyRateLimiter (snakemake.scheduler 中的类)
dynamic() (snakemake.dag.DAG 方法)
(在 snakemake.io 模块中)
dynamic_branch() (snakemake.rules.Rule 方法)
dynamic_input (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
dynamic_output (snakemake.jobs.Job 属性)
dynamic_output_jobs (snakemake.dag.DAG 属性)
dynamic_wildcards (snakemake.jobs.Job 属性)
E
effective_indent (snakemake.parser.TokenAutomaton 属性)
EGAFile (snakemake.remote.EGA 中的类)
EGAFileInfo (snakemake.remote.EGA 中的类)
EmbeddedFigure (snakemake.report 中的类)
EmbeddedImage (snakemake.report 中的类)
EmbeddedMixin (snakemake.report 中的类)
emit() (snakemake.logging.ColorizingStreamHandler 方法)
empty_remote_dirs (snakemake.jobs.Job 属性)
encode_dict() (snakemake.script.JuliaEncoder 类方法)
(snakemake.script.REncoder 类方法)
encode_items() (snakemake.script.JuliaEncoder 类方法)
(snakemake.script.REncoder 类方法)
encode_list() (snakemake.script.JuliaEncoder 类方法)
(snakemake.script.REncoder 类方法)
encode_namedlist() (snakemake.script.JuliaEncoder 类方法)
(snakemake.script.REncoder 类方法)
encode_numeric() (snakemake.script.REncoder 类方法)
encode_positional_items() (snakemake.script.JuliaEncoder 类方法)
encode_value() (snakemake.script.JuliaEncoder 类方法)
(snakemake.script.REncoder 类方法)
end() (snakemake.parser.AbstractCmd 方法)
(snakemake.parser.DecoratorKeywordState 方法)
(snakemake.parser.KeywordState 方法)
(snakemake.parser.Rule 方法)
(snakemake.parser.Run 方法)
(snakemake.parser.Subworkflow 方法)
(snakemake.parser.SubworkflowKeywordState 方法)
end_func (snakemake.parser.AbstractCmd 属性)
(snakemake.parser.CWL 属性)
(snakemake.parser.Script 属性)
(snakemake.parser.Shell 属性)
(snakemake.parser.Wrapper 属性)
Env (snakemake.conda 中的类)
error() (snakemake.logging.Logger 方法)
(snakemake.parser.TokenAutomaton 方法)
error_callback (snakemake.executors.DRMAAClusterJob 属性)
(snakemake.executors.GenericClusterJob 属性)
(snakemake.executors.KubernetesJob 属性)
(snakemake.executors.SynchronousClusterJob 属性)
escape_backslash() (在 snakemake.common 模块中)
executable() (snakemake.shell.shell 类方法)
execute() (snakemake.workflow.Workflow 方法)
existing_output (snakemake.jobs.Job 属性)
existing_remote_input (snakemake.jobs.Job 属性)
existing_remote_output (snakemake.jobs.Job 属性)
exists() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.EGA.RemoteObject 方法)
(snakemake.remote.FTP.RemoteObject 方法)
(snakemake.remote.HTTP.RemoteObject 方法)
(snakemake.remote.S3.RemoteObject 方法)
(snakemake.remote.SFTP.RemoteObject 方法)
(snakemake.remote.StaticRemoteObjectProxy 方法)
(snakemake.remote.dropbox.RemoteObject 方法)
(snakemake.remote.webdav.RemoteObject 方法)
exists_in_bucket() (snakemake.remote.S3.S3Helper 方法)
exit_gracefully() (snakemake.scheduler.JobScheduler 方法)
expand() (在 snakemake.io 模块中)
expand_benchmark() (snakemake.rules.Rule 方法)
expand_conda_env() (snakemake.rules.Rule 方法)
expand_dynamic() (snakemake.jobs.Job 方法)
expand_group() (snakemake.rules.Rule 方法)
expand_input() (snakemake.rules.Rule 方法)
expand_log() (snakemake.rules.Rule 方法)
expand_output() (snakemake.rules.Rule 方法)
expand_params() (snakemake.rules.Rule 方法)
expand_resources() (snakemake.rules.Rule 方法)
expanded_output (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
external_jobids() (snakemake.persistence.Persistence 方法)
F
file() (snakemake.remote.AbstractRemoteObject 方法)
file2jobs() (snakemake.dag.DAG 方法)
file_stats (snakemake.stats.Stats 属性)
FileRecord (snakemake.report 中的类)
files (snakemake.persistence.Persistence 属性)
files_to_download (snakemake.jobs.Job 属性)
files_to_upload (snakemake.jobs.Job 属性)
finalize() (snakemake.jobs.GroupJob 方法)
find_extension() (在 snakemake.wrapper 模块中)
finish() (snakemake.dag.DAG 方法)
finished() (snakemake.dag.DAG 方法)
(snakemake.persistence.Persistence 方法)
finished_jobs (snakemake.dag.DAG 属性)
first_time (snakemake.benchmark.BenchmarkRecord 属性)
flag() (在 snakemake.io 模块中)
forced (snakemake.jobs.Reason 属性)
format() (在 snakemake.utils 模块中)
,
[1]
format_arg() (snakemake.exceptions.WorkflowError 静态方法)
format_dict() (在 snakemake.logging 模块中)
format_element() (snakemake.utils.SequenceFormatter 方法)
,
[1]
format_error() (在 snakemake.exceptions 模块中)
format_field() (snakemake.utils.AlwaysQuotedFormatter 方法)
(snakemake.utils.QuotedFormatter 方法)
(snakemake.utils.SequenceFormatter 方法)
format_files() (在 snakemake.jobs 模块中)
format_job() (snakemake.executors.ClusterExecutor 方法)
format_job_pattern() (snakemake.executors.RealExecutor 方法)
format_resource_names() (在 snakemake.logging 模块中)
format_resources() (在 snakemake.logging 模块中)
(在 snakemake.workflow 模块中)
format_tokens() (在 snakemake.parser 模块中)
format_traceback() (在 snakemake.exceptions 模块中)
format_wildcards() (snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
(在 snakemake.logging 模块中)
ftpc() (snakemake.remote.FTP.RemoteObject 方法)
FTPFileException
G
GenericClusterExecutor (snakemake.executors 中的类)
GenericClusterJob (snakemake.executors 中的类)
get() (snakemake.checkpoints.Checkpoint 方法)
(snakemake.io.Namedlist 方法)
get_appdirs() (在 snakemake 模块中)
get_args() (在 snakemake.gui 模块中)
get_argument_parser() (在 snakemake 模块中)
get_conda_env() (在 snakemake.wrapper 模块中)
get_container_image() (在 snakemake.common 模块中)
get_default_remote_provider_args() (snakemake.executors.AbstractExecutor 方法)
get_exception_origin() (在 snakemake.exceptions 模块中)
get_executable() (snakemake.shell.shell 类方法)
get_executor() (snakemake.scheduler.JobScheduler 方法)
get_files() (snakemake.remote.EGA.RemoteProvider 方法)
get_flag_value() (在 snakemake.io 模块中)
get_git_root() (在 snakemake.io 模块中)
get_git_root_parent_directory() (在 snakemake.io 模块中)
get_header() (snakemake.benchmark.BenchmarkRecord 类方法)
get_header_item() (snakemake.remote.HTTP.RemoteObject 方法)
get_jobs_or_groups() (snakemake.dag.DAG 方法)
get_jobscript() (snakemake.executors.ClusterExecutor 方法)
get_last_stable_version() (在 snakemake.common 模块中)
get_logfile() (snakemake.logging.Logger 方法)
get_names() (snakemake.io.Namedlist 方法)
get_path() (在 snakemake.wrapper 模块中)
get_profile_file() (在 snakemake 模块中)
get_resource_as_string() (在 snakemake.report 模块中)
get_rule() (snakemake.workflow.Workflow 方法)
get_script() (在 snakemake.wrapper 模块中)
get_singularity_envvars() (snakemake.conda.Env 类方法)
get_source() (在 snakemake.script 模块中)
get_sources() (snakemake.workflow.Workflow 方法)
get_targets() (snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
get_uuid() (在 snakemake.common 模块中)
get_wait_for_files() (snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
get_wildcard_len() (snakemake.rules.Rule 静态方法)
get_wildcard_names() (在 snakemake.io 模块中)
get_wildcards() (snakemake.rules.Rule 方法)
git_content() (在 snakemake.io 模块中)
glob_wildcards() (snakemake.remote.AbstractRemoteProvider 方法)
(在 snakemake.io 模块中)
global_singularity() (snakemake.workflow.Workflow 方法)
global_wildcard_constraints() (snakemake.workflow.Workflow 方法)
GlobalKeywordState (snakemake.parser 中的类)
GlobalSingularity (snakemake.parser 中的类)
GlobalWildcardConstraints (snakemake.parser 中的类)
GREEN (snakemake.logging.ColorizingStreamHandler 属性)
group (snakemake.jobs.Job 属性)
Group (snakemake.parser 中的类)
group() (snakemake.workflow.Workflow 方法)
group_error() (snakemake.logging.Logger 方法)
group_info() (snakemake.logging.Logger 方法)
groupid (snakemake.jobs.GroupJob 属性)
GroupJob (snakemake.jobs 中的类)
H
handle_job_error() (snakemake.executors.AbstractExecutor 方法)
(snakemake.executors.CPUExecutor 方法)
(snakemake.executors.ClusterExecutor 方法)
(snakemake.executors.RealExecutor 方法)
handle_job_success() (snakemake.executors.AbstractExecutor 方法)
(snakemake.executors.CPUExecutor 方法)
(snakemake.executors.ClusterExecutor 方法)
(snakemake.executors.RealExecutor 方法)
(snakemake.executors.TouchExecutor 方法)
handle_log() (snakemake.dag.DAG 方法)
handle_pipes() (snakemake.dag.DAG 方法)
handle_protected() (snakemake.dag.DAG 方法)
handle_remote() (snakemake.dag.DAG 方法)
handle_temp() (snakemake.dag.DAG 方法)
handle_touch() (snakemake.dag.DAG 方法)
handler() (snakemake.logging.Logger 方法)
has_wildcards() (snakemake.rules.Rule 方法)
hash (snakemake.conda.Env 属性)
(snakemake.singularity.Image 属性)
HIGHEST_PRIORITY (snakemake.jobs.Job 属性)
host (snakemake.remote.DomainObject 属性)
HTTPFileException
httpr() (snakemake.remote.HTTP.RemoteObject 方法)
I
icon (snakemake.report.FileRecord 属性)
id (snakemake.remote.EGA.EGAFileInfo 属性)
Image (snakemake.singularity 中的类)
ImproperOutputException
ImproperShadowException
in_omitfrom() (snakemake.dag.DAG 方法)
in_until() (snakemake.dag.DAG 方法)
Include (snakemake.parser 中的类)
include() (snakemake.workflow.Workflow 方法)
incomplete() (snakemake.persistence.Persistence 方法)
incomplete_external_jobid() (snakemake.dag.DAG 方法)
incomplete_files (snakemake.dag.DAG 属性)
incomplete_output (snakemake.jobs.Reason 属性)
IncompleteCheckpointException
IncompleteFilesException
indentation() (snakemake.parser.TokenAutomaton 方法)
index() (在 snakemake.gui 模块中)
info() (snakemake.logging.Logger 方法)
init() (snakemake.dag.DAG 方法)
input (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Input (snakemake.parser 中的类)
input (snakemake.rules.Rule 属性)
(snakemake.rules.RuleProxy 属性)
input() (snakemake.persistence.Persistence 方法)
(snakemake.workflow.Workflow 方法)
input_changed() (snakemake.persistence.Persistence 方法)
input_maxtime (snakemake.jobs.Job 属性)
InputFiles (snakemake.io 中的类)
InputFunctionException
inputsize (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
insert_items() (snakemake.io.Namedlist 方法)
instances (snakemake.conda.Conda 属性)
io_in (snakemake.benchmark.BenchmarkRecord 属性)
io_out (snakemake.benchmark.BenchmarkRecord 属性)
IOCache (snakemake.io 中的类)
IOException
IOFile() (在 snakemake.io 模块中)
IOFileException
is_block_end() (snakemake.parser.AbstractCmd 方法)
(snakemake.parser.KeywordState 方法)
(snakemake.parser.Run 方法)
is_branched (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
is_callable() (在 snakemake.io 模块中)
is_checkpoint (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
is_colon() (在 snakemake.parser 模块中)
is_comma() (在 snakemake.parser 模块中)
is_comment() (在 snakemake.parser 模块中)
is_cwl (snakemake.jobs.Job 属性)
is_dedent() (在 snakemake.parser 模块中)
is_eof() (在 snakemake.parser 模块中)
is_flagged() (在 snakemake.io 模块中)
is_git_path() (在 snakemake.wrapper 模块中)
is_greater() (在 snakemake.parser 模块中)
is_group() (snakemake.jobs.AbstractJob 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
is_img (snakemake.report.FileRecord 属性)
is_indent() (在 snakemake.parser 模块中)
is_local (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
(snakemake.singularity.Image 属性)
is_local() (snakemake.workflow.Workflow 方法)
(在 snakemake.wrapper 模块中)
is_name() (在 snakemake.parser 模块中)
is_newer() (snakemake.remote.SFTP.RemoteObject 方法)
(snakemake.remote.StaticRemoteObjectProxy 方法)
is_newline() (在 snakemake.parser 模块中)
is_norun (snakemake.jobs.Job 属性)
is_op() (在 snakemake.parser 模块中)
is_periodic() (snakemake.io.PeriodicityDetector 方法)
is_producer() (snakemake.rules.Rule 方法)
is_rule() (snakemake.workflow.Workflow 方法)
is_run (snakemake.jobs.Job 属性)
is_script (snakemake.jobs.Job 属性)
is_script() (在 snakemake.wrapper 模块中)
is_shadow (snakemake.jobs.Job 属性)
is_shell (snakemake.jobs.Job 属性)
is_string() (在 snakemake.parser 模块中)
is_table (snakemake.report.FileRecord 属性)
is_text (snakemake.report.FileRecord 属性)
is_tty (snakemake.logging.ColorizingStreamHandler 属性)
is_updated (snakemake.jobs.GroupJob 属性)
is_valid() (snakemake.jobs.Job 方法)
is_wrapper (snakemake.jobs.Job 属性)
items() (snakemake.io.Namedlist 方法)
iter_stdout() (snakemake.shell.shell 静态方法)
J
job (snakemake.executors.DRMAAClusterJob 属性)
(snakemake.executors.GenericClusterJob 属性)
(snakemake.executors.KubernetesJob 属性)
(snakemake.executors.SynchronousClusterJob 属性)
Job (snakemake.jobs 中的类)
job_args_and_prepare() (snakemake.executors.CPUExecutor 方法)
job_error() (snakemake.logging.Logger 方法)
job_finished() (snakemake.logging.Logger 方法)
job_info() (snakemake.logging.Logger 方法)
job_reward() (snakemake.scheduler.JobScheduler 方法)
job_selector() (snakemake.scheduler.JobScheduler 方法)
job_to_cwl() (在 snakemake.cwl 模块中)
job_weight() (snakemake.scheduler.JobScheduler 方法)
jobfailed (snakemake.executors.GenericClusterJob 属性)
jobfiles() (在 snakemake.jobs 模块中)
jobfinished (snakemake.executors.GenericClusterJob 属性)
jobid (snakemake.executors.DRMAAClusterJob 属性)
(snakemake.executors.GenericClusterJob 属性)
(snakemake.executors.KubernetesJob 属性)
(snakemake.executors.SynchronousClusterJob 属性)
(snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
jobid() (snakemake.dag.DAG 方法)
JobRecord (snakemake.report 中的类)
jobs (snakemake.dag.DAG 属性)
(snakemake.jobs.GroupJob 属性)
JobScheduler (snakemake.scheduler 中的类)
jobscript (snakemake.executors.DRMAAClusterJob 属性)
(snakemake.executors.GenericClusterJob 属性)
(snakemake.executors.KubernetesJob 属性)
(snakemake.executors.SynchronousClusterJob 属性)
JuliaEncoder (snakemake.script 中的类)
K
key_last_modified() (snakemake.remote.S3.S3Helper 方法)
key_size() (snakemake.remote.S3.S3Helper 方法)
keys() (snakemake.io.Namedlist 方法)
keyword (snakemake.parser.GlobalSingularity 属性)
(snakemake.parser.GlobalWildcardConstraints 属性)
(snakemake.parser.KeywordState 属性)
(snakemake.parser.WildcardConstraints 属性)
KeywordState (snakemake.parser 中的类)
kill() (snakemake.shell.shell 类方法)
kubejob (snakemake.executors.KubernetesJob 属性)
KubernetesExecutor (snakemake.executors 中的类)
KubernetesJob (snakemake.executors 中的类)
L
lazy_property (snakemake.common 中的类)
lchmod() (在 snakemake.io 模块中)
level_bfs() (snakemake.dag.DAG 方法)
limit() (在 snakemake.io 模块中)
linecount() (在 snakemake.utils 模块中)
,
[1]
lineno() (在 snakemake.parser 模块中)
list (snakemake.remote.dropbox.RemoteObject 属性)
(snakemake.remote.FTP.RemoteObject 属性)
(snakemake.remote.HTTP.RemoteObject 属性)
(snakemake.remote.S3.RemoteObject 属性)
(snakemake.remote.SFTP.RemoteObject 属性)
(snakemake.remote.webdav.RemoteObject 属性)
list() (snakemake.remote.AbstractRemoteObject 方法)
list_keys() (snakemake.remote.S3.S3Helper 方法)
list_resources() (snakemake.workflow.Workflow 方法)
list_rules() (snakemake.workflow.Workflow 方法)
list_untracked() (snakemake.dag.DAG 方法)
listfiles() (在 snakemake.utils 模块中)
,
[1]
load_configfile() (在 snakemake.io 模块中)
local() (在 snakemake.io 模块中)
local_file() (snakemake.remote.AbstractRemoteObject 方法)
local_input (snakemake.jobs.Job 属性)
local_needrun_jobs (snakemake.dag.DAG 属性)
local_output (snakemake.jobs.Job 属性)
local_path (snakemake.remote.DomainObject 属性)
local_touch_or_create() (snakemake.remote.AbstractRemoteObject 方法)
Localrules (snakemake.parser 中的类)
localrules() (snakemake.workflow.Workflow 方法)
location() (snakemake.logging.Logger 方法)
lock() (snakemake.persistence.Persistence 方法)
lock_warn_only() (snakemake.persistence.Persistence 方法)
locked (snakemake.persistence.Persistence 属性)
Log (snakemake.io 中的类)
log (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Log (snakemake.parser 中的类)
log (snakemake.rules.Rule 属性)
(snakemake.rules.RuleProxy 属性)
log() (snakemake.persistence.Persistence 方法)
(snakemake.workflow.Workflow 方法)
(在 snakemake.gui 模块中)
log_error() (snakemake.jobs.AbstractJob 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
log_fmt_shell() (snakemake.script.Snakemake 方法)
log_info() (snakemake.jobs.AbstractJob 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
log_location() (在 snakemake.common 模块中)
log_verbose_traceback() (在 snakemake.exceptions 模块中)
logfile_hint() (snakemake.logging.Logger 方法)
Logger (snakemake.logging 中的类)
lstat() (在 snakemake.io 模块中)
lutime() (在 snakemake.io 模块中)
M
MAGENTA (snakemake.logging.ColorizingStreamHandler 属性)
main() (在 snakemake 模块中)
makedirs() (在 snakemake.utils 模块中)
,
[1]
match() (snakemake.output_index.OutputIndex 方法)
max_pss (snakemake.benchmark.BenchmarkRecord 属性)
max_rss (snakemake.benchmark.BenchmarkRecord 属性)
max_uss (snakemake.benchmark.BenchmarkRecord 属性)
max_vms (snakemake.benchmark.BenchmarkRecord 属性)
merge() (snakemake.jobs.GroupJob 方法)
message (snakemake.jobs.Job 属性)
Message (snakemake.parser 中的类)
message() (snakemake.workflow.Workflow 方法)
messages (snakemake.exceptions.RuleException 属性)
metadata() (snakemake.persistence.Persistence 方法)
method (snakemake.common.lazy_property 属性)
mime_from_file() (在 snakemake.report 模块中)
min_version() (在 snakemake.utils 模块中)
,
[1]
missing_input (snakemake.jobs.Job 属性)
missing_output (snakemake.jobs.Reason 属性)
missing_output() (snakemake.jobs.Job 方法)
missing_remote_input (snakemake.jobs.Job 属性)
missing_remote_output (snakemake.jobs.Job 属性)
missing_temp() (snakemake.dag.DAG 方法)
MissingInputException
MissingOutputException
MissingRuleException
Mode (snakemake.common 中的类)
mtime() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.EGA.RemoteObject 方法)
(snakemake.remote.FTP.RemoteObject 方法)
(snakemake.remote.HTTP.RemoteObject 方法)
(snakemake.remote.S3.RemoteObject 方法)
(snakemake.remote.SFTP.RemoteObject 方法)
(snakemake.remote.StaticRemoteObjectProxy 方法)
(snakemake.remote.dropbox.RemoteObject 方法)
(snakemake.remote.webdav.RemoteObject 方法)
N
name (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
(snakemake.remote.DomainObject 属性)
(snakemake.remote.S3.RemoteObject 属性)
(snakemake.remote.dropbox.RemoteObject 属性)
(snakemake.remote.webdav.RemoteObject 属性)
(snakemake.report.FileRecord 属性)
name() (snakemake.parser.Rule 方法)
(snakemake.parser.Subworkflow 方法)
(snakemake.remote.AbstractRemoteObject 方法)
Namedlist (snakemake.io 中的类)
NCBIFileException
needrun() (snakemake.dag.DAG 方法)
needrun_jobs (snakemake.dag.DAG 属性)
needs_singularity (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
new_job() (snakemake.dag.DAG 方法)
new_wildcards() (snakemake.dag.DAG 方法)
newversion_files (snakemake.dag.DAG 属性)
noio (snakemake.jobs.Reason 属性)
noneedrun_finished() (snakemake.dag.DAG 方法)
noop() (snakemake.persistence.Persistence 方法)
nooutput (snakemake.jobs.Reason 属性)
NoRulesException
norun() (snakemake.workflow.Workflow 方法)
not_iterable() (在 snakemake.io 模块中)
num_if_possible() (在 snakemake.common 模块中)
O
omitfrom_jobs() (snakemake.dag.DAG 方法)
OnError (snakemake.parser 中的类)
onerror() (snakemake.workflow.Workflow 方法)
OnStart (snakemake.parser 中的类)
onstart() (snakemake.workflow.Workflow 方法)
OnSuccess (snakemake.parser 中的类)
onsuccess() (snakemake.workflow.Workflow 方法)
open_jobs (snakemake.scheduler.JobScheduler 属性)
output (snakemake.checkpoints.CheckpointJob 属性)
(snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Output (snakemake.parser 中的类)
output (snakemake.rules.Rule 属性)
(snakemake.rules.RuleProxy 属性)
output() (snakemake.workflow.Workflow 方法)
output_mintime (snakemake.jobs.Job 属性)
output_mintime_local (snakemake.jobs.Job 属性)
OutputFiles (snakemake.io 中的类)
OutputIndex (snakemake.output_index 中的类)
outputs_older_than_script() (snakemake.jobs.Job 方法)
overall_runtime (snakemake.stats.Stats 属性)
overwrite_block_content() (snakemake.parser.AbstractCmd 方法)
overwrite_cmd (snakemake.parser.AbstractCmd 属性)
P
Params (snakemake.io 中的类)
params (snakemake.jobs.Job 属性)
Params (snakemake.parser 中的类)
params (snakemake.rules.Rule 属性)
(snakemake.rules.RuleProxy 属性)
params() (snakemake.persistence.Persistence 方法)
(snakemake.workflow.Workflow 方法)
params_changed() (snakemake.persistence.Persistence 方法)
parse() (在 snakemake.parser 模块中)
parse_config() (在 snakemake 模块中)
parse_default_resources() (在 snakemake 模块中)
parse_resources() (在 snakemake 模块中)
parts (snakemake.remote.EGA.RemoteObject 属性)
path (snakemake.conda.Env 属性)
(snakemake.remote.EGA.EGAFile 属性)
(snakemake.singularity.Image 属性)
path_prefix (snakemake.remote.DomainObject 属性)
path_remainder (snakemake.remote.DomainObject 属性)
PeriodicityDetector (snakemake.io 中的类)
PeriodicWildcardError
Persistence (snakemake.persistence 中的类)
pickle_code() (在 snakemake.persistence 模块中)
pid (snakemake.benchmark.BenchmarkTimer 属性)
pipe() (在 snakemake.io 模块中)
plainstrings() (snakemake.io.Namedlist 方法)
port (snakemake.remote.DomainObject 属性)
postprocess() (snakemake.dag.DAG 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
prefix (snakemake.parser.KeywordState 属性)
(snakemake.parser.SubworkflowKeywordState 属性)
prefix() (snakemake.shell.shell 类方法)
prefix_path() (snakemake.conda.Conda 方法)
prepare() (snakemake.jobs.Job 方法)
prev_time (snakemake.benchmark.BenchmarkRecord 属性)
print_benchmark_records() (在 snakemake.benchmark 模块中)
print_cluster_job_error() (snakemake.executors.ClusterExecutor 方法)
print_exception() (在 snakemake.exceptions 模块中)
print_job_error() (snakemake.executors.AbstractExecutor 方法)
printjob() (snakemake.executors.AbstractExecutor 方法)
priority (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Priority (snakemake.parser 中的类)
priority() (snakemake.dag.DAG 方法)
(snakemake.workflow.Workflow 方法)
process (snakemake.executors.SynchronousClusterJob 属性)
products (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
(snakemake.rules.Rule 属性)
progress() (snakemake.logging.Logger 方法)
(snakemake.scheduler.JobScheduler 方法)
(在 snakemake.gui 模块中)
properties() (snakemake.jobs.AbstractJob 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
protected() (在 snakemake.io 模块中)
protected_output (snakemake.jobs.Job 属性)
ProtectedOutputException
pull() (snakemake.singularity.Image 方法)
pull_singularity_imgs() (snakemake.dag.DAG 方法)
Python (snakemake.parser 中的类)
python() (snakemake.parser.Python 方法)
Q
QuotedFormatter (snakemake.utils 中的类)
,
[1]
R
R() (在 snakemake.utils 模块中)
,
[1]
read_job_properties() (在 snakemake.utils 模块中)
,
[1]
ready_jobs (snakemake.dag.DAG 属性)
RealExecutor (snakemake.executors 中的类)
Reason (snakemake.jobs 中的类)
reason() (snakemake.dag.DAG 方法)
RED (snakemake.logging.ColorizingStreamHandler 属性)
regex() (在 snakemake.io 模块中)
register() (snakemake.checkpoints.Checkpoints 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
(在 snakemake.gui 模块中)
register_job() (snakemake.executors.GenericClusterExecutor 方法)
(snakemake.executors.RealExecutor 方法)
register_secret() (snakemake.executors.KubernetesExecutor 方法)
register_wildcards() (snakemake.rules.Rule 方法)
remote() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.AbstractRemoteProvider 方法)
(snakemake.remote.FTP.RemoteProvider 方法)
(snakemake.remote.HTTP.RemoteProvider 方法)
remote_file() (snakemake.remote.AbstractRemoteObject 方法)
remote_input (snakemake.jobs.Job 属性)
remote_input_newer_than_local (snakemake.jobs.Job 属性)
remote_input_older_than_local (snakemake.jobs.Job 属性)
remote_interface() (snakemake.remote.AbstractRemoteProvider 方法)
(snakemake.remote.S3.RemoteProvider 方法)
(snakemake.remote.dropbox.RemoteProvider 方法)
remote_output (snakemake.jobs.Job 属性)
remote_output_newer_than_local (snakemake.jobs.Job 属性)
remote_output_older_than_local (snakemake.jobs.Job 属性)
remote_path (snakemake.remote.DomainObject 属性)
RemoteFileException
RemoteObject (snakemake.remote.dropbox 中的类)
(snakemake.remote.EGA 中的类)
(snakemake.remote.FTP 中的类)
(snakemake.remote.HTTP 中的类)
(snakemake.remote.S3 中的类)
(snakemake.remote.SFTP 中的类)
(snakemake.remote.webdav 中的类)
RemoteProvider (snakemake.remote.dropbox 中的类)
(snakemake.remote.EGA 中的类)
(snakemake.remote.FTP 中的类)
(snakemake.remote.HTTP 中的类)
(snakemake.remote.S3 中的类)
(snakemake.remote.SFTP 中的类)
(snakemake.remote.webdav 中的类)
remove() (snakemake.remote.AbstractRemoteObject 方法)
(在 snakemake.io 模块中)
remove_existing_output() (snakemake.jobs.AbstractJob 方法)
(snakemake.jobs.GroupJob 方法)
(snakemake.jobs.Job 方法)
remove_logfile() (snakemake.logging.Logger 方法)
REncoder (snakemake.script 中的类)
render() (snakemake.report.FileRecord 方法)
repeat() (在 snakemake.io 模块中)
replace_job() (snakemake.dag.DAG 方法)
Report (snakemake.parser 中的类)
report() (snakemake.workflow.Workflow 方法)
(在 snakemake.io 模块中)
(在 snakemake.report 模块中)
(在 snakemake.utils 模块中)
,
[1]
report_job_end() (snakemake.stats.Stats 方法)
report_job_start() (snakemake.stats.Stats 方法)
ReportObject (snakemake.io 中的类)
requested_files() (snakemake.dag.DAG 方法)
RESET_SEQ (snakemake.logging.ColorizingStreamHandler 属性)
Resources (snakemake.io 中的类)
resources (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Resources (snakemake.parser 中的类)
resources() (snakemake.workflow.Workflow 方法)
resources_info() (snakemake.logging.Logger 方法)
restart_times (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
rmdir_empty_remote_dirs() (snakemake.jobs.Job 方法)
rule (snakemake.checkpoints.Checkpoint 属性)
(snakemake.checkpoints.CheckpointJob 属性)
(snakemake.jobs.Job 属性)
Rule (snakemake.parser 中的类)
(snakemake.rules 中的类)
rule() (snakemake.persistence.Persistence 方法)
(snakemake.workflow.Workflow 方法)
rule2job() (snakemake.dag.DAG 方法)
rule_dot() (snakemake.dag.DAG 方法)
rule_dot2() (snakemake.dag.DAG 方法)
rule_info() (snakemake.logging.Logger 方法)
rule_prefix() (snakemake.executors.AbstractExecutor 方法)
rule_stats (snakemake.stats.Stats 属性)
rule_weight() (snakemake.scheduler.JobScheduler 方法)
RuleException
rulegraph_d3_spec() (在 snakemake.report 模块中)
RuleInfo (snakemake.workflow 中的类)
RuleKeywordState (snakemake.parser 中的类)
Ruleorder (snakemake.parser 中的类)
(snakemake.rules 中的类)
ruleorder() (snakemake.workflow.Workflow 方法)
RuleProxy (snakemake.rules 中的类)
RuleRecord (snakemake.report 中的类)
rules (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Rules (snakemake.workflow 中的类)
rules (snakemake.workflow.Workflow 属性)
Run (snakemake.parser 中的类)
run() (snakemake.benchmark.DaemonTimer 方法)
(snakemake.executors.AbstractExecutor 方法)
(snakemake.executors.CPUExecutor 方法)
(snakemake.executors.DRMAAExecutor 方法)
(snakemake.executors.GenericClusterExecutor 方法)
(snakemake.executors.KubernetesExecutor 方法)
(snakemake.executors.SynchronousClusterExecutor 方法)
(snakemake.executors.TouchExecutor 方法)
(snakemake.report.EmbeddedMixin 方法)
(snakemake.scheduler.JobScheduler 方法)
(snakemake.workflow.Workflow 方法)
(在 snakemake.gui 模块中)
run_group_job() (snakemake.executors.CPUExecutor 方法)
run_info() (snakemake.logging.Logger 方法)
run_single_job() (snakemake.executors.CPUExecutor 方法)
run_snakemake() (在 snakemake.gui 模块中)
run_wrapper() (在 snakemake.executors 模块中)
running_time (snakemake.benchmark.BenchmarkRecord 属性)
S
s3_bucket (snakemake.remote.S3.RemoteObject 属性)
s3_create_stub() (snakemake.remote.S3.RemoteObject 方法)
s3_key (snakemake.remote.S3.RemoteObject 属性)
S3FileException
S3Helper (snakemake.remote.S3 中的类)
schedule() (snakemake.scheduler.JobScheduler 方法)
ScheduledPeriodicTimer (snakemake.benchmark 中的类)
Script (snakemake.parser 中的类)
script() (snakemake.workflow.Workflow 方法)
(在 snakemake.script 模块中)
SequenceFormatter (snakemake.utils 中的类)
,
[1]
set_args() (在 snakemake.gui 模块中)
set_input() (snakemake.rules.Rule 方法)
set_level() (snakemake.logging.Logger 方法)
set_log() (snakemake.rules.Rule 方法)
set_name() (snakemake.io.Namedlist 方法)
set_output() (snakemake.rules.Rule 方法)
set_params() (snakemake.rules.Rule 方法)
set_stream_handler() (snakemake.logging.Logger 方法)
set_until_jobs() (snakemake.dag.DAG 方法)
set_wildcard_constraints() (snakemake.rules.Rule 方法)
setup_logfile() (snakemake.logging.Logger 方法)
setup_logger() (在 snakemake.logging 模块中)
sftpc() (snakemake.remote.SFTP.RemoteObject 方法)
SFTPFileException
Shadow (snakemake.parser 中的类)
shadow() (snakemake.workflow.Workflow 方法)
shadow_dir (snakemake.jobs.Job 属性)
shadowed_path() (snakemake.jobs.Job 方法)
Shell (snakemake.parser 中的类)
shell (snakemake.shell 中的类)
shellcmd (snakemake.jobs.Job 属性)
shellcmd() (snakemake.conda.Conda 方法)
(snakemake.logging.Logger 方法)
(snakemake.persistence.Persistence 方法)
(snakemake.workflow.Workflow 方法)
(在 snakemake.singularity 模块中)
shutdown() (snakemake.executors.AbstractExecutor 方法)
(snakemake.executors.CPUExecutor 方法)
(snakemake.executors.ClusterExecutor 方法)
(snakemake.executors.DRMAAExecutor 方法)
(snakemake.executors.KubernetesExecutor 方法)
simplify_path() (在 snakemake.utils 模块中)
,
[1]
Singularity (snakemake.parser 中的类)
singularity() (snakemake.workflow.Workflow 方法)
singularity_img (snakemake.jobs.Job 属性)
(snakemake.rules.Rule 属性)
singularity_img_path (snakemake.jobs.Job 属性)
singularity_img_url (snakemake.conda.Env 属性)
(snakemake.jobs.Job 属性)
size (snakemake.io.InputFiles 属性)
(snakemake.remote.EGA.EGAFileInfo 属性)
size() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.EGA.RemoteObject 方法)
(snakemake.remote.FTP.RemoteObject 方法)
(snakemake.remote.HTTP.RemoteObject 方法)
(snakemake.remote.S3.RemoteObject 方法)
(snakemake.remote.SFTP.RemoteObject 方法)
(snakemake.remote.dropbox.RemoteObject 方法)
(snakemake.remote.webdav.RemoteObject 方法)
sleep() (在 snakemake.executors 模块中)
Snakefile (snakemake.parser 中的类)
snakefile (snakemake.workflow.Subworkflow 属性)
Snakemake (snakemake.script 中的类)
snakemake (模块)
snakemake() (在 snakemake 模块中)
,
[1]
snakemake.benchmark (模块)
snakemake.checkpoints (模块)
snakemake.common (模块)
snakemake.conda (模块)
snakemake.cwl (模块)
snakemake.dag (模块)
snakemake.decorators (模块)
snakemake.exceptions (模块)
snakemake.executors (模块)
snakemake.gui (模块)
snakemake.io (模块)
snakemake.jobs (模块)
snakemake.logging (模块)
snakemake.output_index (模块)
snakemake.parser (模块)
snakemake.persistence (模块)
snakemake.remote (模块)
snakemake.remote.dropbox (模块)
snakemake.remote.EGA (模块)
snakemake.remote.FTP (模块)
snakemake.remote.HTTP (模块)
snakemake.remote.S3 (模块)
snakemake.remote.SFTP (模块)
snakemake.remote.webdav (模块)
snakemake.report (模块)
snakemake.rules (模块)
snakemake.scheduler (模块)
snakemake.script (模块)
snakemake.shell (模块)
snakemake.singularity (模块)
snakemake.stats (模块)
snakemake.utils (模块)
,
[1]
snakemake.workflow (模块)
snakemake.wrapper (模块)
spawn_job() (snakemake.executors.CPUExecutor 方法)
SpawnedJobError
specialize_rule() (snakemake.dag.DAG 方法)
split_git_path() (在 snakemake.io 模块中)
srcdir() (在 snakemake.workflow 模块中)
start() (snakemake.benchmark.ScheduledPeriodicTimer 方法)
(snakemake.parser.AbstractCmd 方法)
(snakemake.parser.Checkpoint 方法)
(snakemake.parser.DecoratorKeywordState 方法)
(snakemake.parser.GlobalKeywordState 方法)
(snakemake.parser.Rule 方法)
(snakemake.parser.RuleKeywordState 方法)
(snakemake.parser.Run 方法)
(snakemake.parser.SubworkflowKeywordState 方法)
start_func (snakemake.parser.AbstractCmd 属性)
(snakemake.parser.CWL 属性)
(snakemake.parser.Script 属性)
(snakemake.parser.Shell 属性)
(snakemake.parser.Wrapper 属性)
started() (snakemake.persistence.Persistence 方法)
StaticRemoteObjectProxy (snakemake.remote 中的类)
stats (snakemake.scheduler.JobScheduler 属性)
Stats (snakemake.stats 中的类)
stats() (snakemake.dag.DAG 方法)
status (snakemake.remote.EGA.EGAFileInfo 属性)
status() (在 snakemake.gui 模块中)
StopAutomaton
strip_prefix() (在 snakemake.common 模块中)
strip_wildcard_constraints() (在 snakemake.io 模块中)
stripped_constraints() (snakemake.io.Namedlist 方法)
subautomata (snakemake.parser.Python 属性)
(snakemake.parser.Rule 属性)
(snakemake.parser.Subworkflow 属性)
(snakemake.parser.TokenAutomaton 属性)
subautomaton() (snakemake.parser.TokenAutomaton 方法)
subprocess (snakemake.common.Mode 属性)
Subworkflow (snakemake.parser 中的类)
(snakemake.workflow 中的类)
subworkflow() (snakemake.workflow.Workflow 方法)
subworkflow_input (snakemake.jobs.Job 属性)
SubworkflowConfigfile (snakemake.parser 中的类)
SubworkflowKeywordState (snakemake.parser 中的类)
subworkflows (snakemake.workflow.Workflow 属性)
SubworkflowSnakefile (snakemake.parser 中的类)
SubworkflowWorkdir (snakemake.parser 中的类)
suffix() (snakemake.shell.shell 类方法)
summary() (snakemake.dag.DAG 方法)
supports_default (snakemake.remote.AbstractRemoteProvider 属性)
(snakemake.remote.FTP.RemoteProvider 属性)
(snakemake.remote.S3.RemoteProvider 属性)
(snakemake.remote.SFTP.RemoteProvider 属性)
SynchronousClusterExecutor (snakemake.executors 中的类)
SynchronousClusterJob (snakemake.executors 中的类)
T
take_names() (snakemake.io.Namedlist 方法)
target() (snakemake.workflow.Subworkflow 方法)
targetfile (snakemake.jobs.Job 属性)
targets() (snakemake.workflow.Subworkflow 方法)
(在 snakemake.gui 模块中)
temp() (在 snakemake.io 模块中)
temp_input() (snakemake.dag.DAG 方法)
temp_output (snakemake.jobs.Job 属性)
temp_size() (snakemake.dag.DAG 方法)
temporary() (在 snakemake.io 模块中)
TerminatedException
text_handler() (snakemake.logging.Logger 方法)
threads (snakemake.jobs.GroupJob 属性)
(snakemake.jobs.Job 属性)
Threads (snakemake.parser 中的类)
threads() (snakemake.workflow.Workflow 方法)
tmpdir (snakemake.executors.ClusterExecutor 属性)
to_json() (snakemake.stats.Stats 方法)
to_tsv() (snakemake.benchmark.BenchmarkRecord 方法)
token (snakemake.remote.EGA.RemoteProvider 属性)
TokenAutomaton (snakemake.parser 中的类)
touch() (在 snakemake.io 模块中)
touch_output (snakemake.jobs.Job 属性)
TouchExecutor (snakemake.executors 中的类)
U
UnexpectedOutputException
Unformattable (snakemake.utils 中的类)
unique_input (snakemake.jobs.Job 属性)
UnknownRuleException
unlock() (snakemake.persistence.Persistence 方法)
unpack() (在 snakemake.io 模块中)
unparse_config() (在 snakemake 模块中)
unregister_secret() (snakemake.executors.KubernetesExecutor 方法)
unshadow_output() (snakemake.dag.DAG 方法)
until_jobs() (snakemake.dag.DAG 方法)
update() (snakemake.dag.DAG 方法)
update_() (snakemake.dag.DAG 方法)
update_checkpoint_dependencies() (snakemake.dag.DAG 方法)
update_checkpoint_outputs() (snakemake.dag.DAG 方法)
update_config() (在 snakemake.utils 模块中)
,
[1]
update_dynamic() (snakemake.dag.DAG 方法)
update_groups() (snakemake.dag.DAG 方法)
update_jobids() (snakemake.dag.DAG 方法)
update_needrun() (snakemake.dag.DAG 方法)
update_output_index() (snakemake.dag.DAG 方法)
update_priority() (snakemake.dag.DAG 方法)
update_ready() (snakemake.dag.DAG 方法)
update_wildcard_constraints() (snakemake.rules.Rule 方法)
(在 snakemake.io 模块中)
updated() (snakemake.jobs.Job 方法)
updated_input (snakemake.jobs.Reason 属性)
updated_input_run (snakemake.jobs.Reason 属性)
upload() (snakemake.remote.AbstractRemoteObject 方法)
(snakemake.remote.FTP.RemoteObject 方法)
(snakemake.remote.HTTP.RemoteObject 方法)
(snakemake.remote.S3.RemoteObject 方法)
(snakemake.remote.SFTP.RemoteObject 方法)
(snakemake.remote.dropbox.RemoteObject 方法)
(snakemake.remote.webdav.RemoteObject 方法)
upload_to_s3() (snakemake.remote.S3.S3Helper 方法)
V
validate() (在 snakemake.utils 模块中)
,
[1]
Version (snakemake.parser 中的类)
version (snakemake.rules.Rule 属性)
version() (snakemake.persistence.Persistence 方法)
(snakemake.workflow.Workflow 方法)
version_changed() (snakemake.persistence.Persistence 方法)
W
wait_for_files() (在 snakemake.io 模块中)
warning() (snakemake.logging.Logger 方法)
webdav_file (snakemake.remote.webdav.RemoteObject 属性)
webdavc() (snakemake.remote.webdav.RemoteObject 方法)
WebDAVFileException
WHITE (snakemake.logging.ColorizingStreamHandler 属性)
wildcard_constraints (snakemake.rules.Rule 属性)
wildcard_constraints() (snakemake.workflow.Workflow 方法)
wildcard_names (snakemake.rules.Rule 属性)
WildcardConstraints (snakemake.parser 中的类)
WildcardError
Wildcards (snakemake.io 中的类)
wildcards (snakemake.jobs.Job 属性)
wildcards_dict (snakemake.jobs.Job 属性)
work() (snakemake.benchmark.BenchmarkTimer 方法)
(snakemake.benchmark.ScheduledPeriodicTimer 方法)
Workdir (snakemake.parser 中的类)
workdir (snakemake.workflow.Subworkflow 属性)
workdir() (snakemake.workflow.Workflow 方法)
Workflow (snakemake.workflow 中的类)
WorkflowError
Wrapper (snakemake.parser 中的类)
wrapper() (snakemake.workflow.Workflow 方法)
(在 snakemake.wrapper 模块中)
write_benchmark_records() (在 snakemake.benchmark 模块中)
write_jobscript() (snakemake.executors.ClusterExecutor 方法)
X
XRootDFileException
Y
YELLOW (snakemake.logging.ColorizingStreamHandler 属性)
yield_indent() (snakemake.parser.KeywordState 方法)