snakemake.io

Functions

IOFile(file[, rule])
ancient(value)	A flag for an input file that shall be considered ancient; i.e. its timestamp shall have no effect on which jobs to run.
apply_wildcards(pattern, wildcards)
checkpoint_target(value)
contains_wildcard(path)
contains_wildcard_constraints(pattern)
directory(value)	A flag to specify that output is a directory, rather than a file or named pipe.
ensure(value[, non_empty, sha256])
expand(*args, **wildcard_values)	Expand wildcards in given filepatterns.
flag(value, flag_type[, flag_value])
from_queue(queue[, finish_sentinel])
get_flag_value(value, flag_type)
get_wildcard_constraints(pattern)
get_wildcard_names(pattern)
glob_wildcards(pattern[, files, followlinks])	Glob the values of the wildcards by matching the given pattern to the filesystem.
iocache(func)
is_callable(value)
is_flagged(value, flag)	rtype: bool
limit(pattern, **wildcards)	Limit wildcards to the given values.
local(value)	Mark a file as a local file.
lutime(file, times)
multiext(prefix, *extensions)	Expand a given prefix with multiple extensions (e.g. .txt, .csv, _peaks.bed, ...).
pipe(value)
pretty_print_iofile(iofile)
protected(value)	A flag for a file that shall be write-protected after creation.
regex_from_filepattern(filepattern)
remove(file[, remove_non_empty_dir, only_local])
repeat(value, n_repeat)	Flag benchmark records with the number of repeats.
report(value[, caption, category, ...])	Flag output file or directory as to be included into reports.
service(value)
sourcecache_entry(value, orig_path_or_uri)
strip_wildcard_constraints(pattern)	Return a string that does not contain any wildcard constraints.
temp(value)	A flag for an input or output file that shall be removed after usage.
temporary(value)	An alias for temp.
touch(value)
unpack(value)
update_wildcard_constraints(pattern, ...)	Update wildcard constraints
wait_for_files(files[, latency_wait, ...])	Wait for given files to be present in the filesystem.

Classes

AnnotatedString(value)
AnnotatedStringInterface()
ExistsDict(cache)
IOCache(max_wait_time)
InputFiles([toclone, fromdict, plainstr, ...])
Log([toclone, fromdict, plainstr, ...])
Namedlist([toclone, fromdict, plainstr, ...])	A list that additionally provides functions to name items.
OutputFiles([toclone, fromdict, plainstr, ...])
Params([toclone, fromdict, plainstr, ...])
PeriodicityDetector([min_repeat, max_repeat])
QueueInfo(queue, finish_sentinel[, ...])
ReportObject(caption, category, subcategory, ...)
Resources([toclone, fromdict, plainstr, ...])
Wildcards([toclone, fromdict, plainstr, ...])