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Index
Symbols
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A
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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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I
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J
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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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R
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S
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T
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U
Symbols
@active_if
Syntax
Tutorial
@check_if_uptodate
Syntax
@collate
Syntax
Tutorial
@collate (Advanced Usage)
Syntax
@collate, add_inputs(...)
Syntax
@collate, inputs(...)
Syntax
@combinations
Syntax
@combinations_with_replacement
Syntax
@files
Manual
Syntax
Tutorial on-the-fly parameter generation
check if up to date
in parallel
@files (on-the-fly parameter generation)
Syntax
@files_re
Syntax
combine (Deprecated Syntax)
@follow
imposing order with
@follows
Syntax
mkdir (Manual)
mkdir (Syntax)
@graphviz
Syntax
@jobs_limit
Syntax
Tutorial
@merge
Syntax
@mkdir
Syntax
@originate
Syntax
@parallel
Syntax
Tutorial
@permutations
Syntax
@posttask
Syntax
touch_file (Syntax)
touchfile (Manual)
@product
Syntax
@split
Syntax
@subdivide
Syntax
Tutorial
@transform
Syntax
multiple dependencies
@transform, add_inputs(...)
Syntax
@transform, inputs(...)
Syntax
A
Acknowledgements
add_inputs
Indicator Object (Adding additional input parameters)
Tutorial
args_param_factory() (in module ruffus.task)
B
break
C
check if up to date
@files
check_if_uptodate
Tutorial
Checking dependencies
Tutorial
collate_param_factory() (in module ruffus.task)
combinatorics
Tutorial
combine
@follows (Deprecated Syntax)
Manual
command line
Tutorial
Comparison of Ruffus with alternatives
Design
D
data sharing across processes
Tutorial
decorator
decorators_compendium
Tutorial
defining tasks out of order
output_from
deprecated @files
Tutorial
deprecated @files_re
Tutorial
Design
Comparison of Ruffus with alternatives
Ruffus
drmaa
run_job
E
errors
Etymology
Ruffus
Exception
Missing input files
Exceptions
Tutorial
exceptions
Tutorial
F
files_param_factory() (in module ruffus.task)
flag files
Manual
flowchart colours
Tutorial
,
[1]
for rerunning jobs
rules
formatter
Indicator Object (Disambiguating parameters)
Tutorial
G
generator
globs
inputs parameters
globs in input parameters
Tutorial
I
importing ruffus
imposing order with
@follow
in parallel
@files
Indicator Object (Adding additional input parameters)
add_inputs
Indicator Object (Disambiguating parameters)
combine
formatter
mkdir
output_from
regex
suffix
touch_file
Indicator Object (Replacing input parameters)
inputs
input / output parameters
Tutorial
inputs
Indicator Object (Replacing input parameters)
Tutorial
inputs parameters
globs
Interrupted Pipeline
Tutorial
interrupting tasks
Tutorial
interrupts
J
job
job_wrapper_generic() (in module ruffus.task)
job_wrapper_io_files() (in module ruffus.task)
job_wrapper_mkdir() (in module ruffus.task)
L
logging
Tutorial
logging customising
Tutorial
logging with ruffus.cmdline
Tutorial
logging your own message
Tutorial
M
make_shared_logger_and_proxy() (in module ruffus.proxy_logger)
Manual
@files
Timestamp resolution
combine
flag files
merge
Tutorial
merge_param_factory() (in module ruffus.task)
Missing input files
Exception
Mixing tasks, globs and file names
Tutorial
mkdir
@follows (Manual)
@follows (Syntax)
Tutorial
multiple dependencies
@transform
multiple errors
multiprocessing
Tutorial
N
Name origins
Ruffus
needs_update_check_directory_missing() (in module ruffus.task)
needs_update_check_modify_time() (in module ruffus.task)
O
on_the_fly
Tutorial
one to one @transform
Tutorial
originate
Tutorial
output file names
Tutorial
output_from
Indicator Object (Disambiguating parameters)
defining tasks out of order
referring to functions before they are defined
overview
Tutorial
P
pipeline functions
pipeline_get_task_names
pipeline_printout_graph
pipeline_run
,
[1]
pipeline_get_task_names
print list of task names without running the pipeline
pipeline_printout
Printout simulated run of the pipeline
Tutorial
pipeline_printout() (in module ruffus.task)
pipeline_printout_graph
Tutorial
print flowchart representation of pipeline functions
pipeline_printout_graph() (in module ruffus.task)
pipeline_run
Run pipeline
Tutorial
pipeline_run touch mode
Tutorial
pipeline_run verbosity
Tutorial
pipeline_run() (in module ruffus.task)
pipeline_run(multiprocess)
Tutorial
posttask
Tutorial
print flowchart representation of pipeline functions
pipeline_printout_graph
print list of task names without running the pipeline
pipeline_get_task_names
Printout simulated run of the pipeline
pipeline_printout
R
referring to functions before they are defined
output_from
Regenerating the checkpoint file
Tutorial
regex
Indicator Object (Disambiguating parameters)
Tutorial
Ruffus
Design
Etymology
Name origins
Ruffus names list
Tutorial
ruffus.proxy_logger (module)
rules
for rerunning jobs
Run drmaa
run_job
Run pipeline
pipeline_run
run_job
Run drmaa
S
setup_std_shared_logger() (in module ruffus.proxy_logger)
signalling
split
Tutorial
split_param_factory() (in module ruffus.task)
string substiution for inputs
Tutorial
suffix
Indicator Object (Disambiguating parameters)
Tutorial
Syntax
@active_if
@check_if_uptodate
@collate
@collate (Advanced Usage)
@collate, add_inputs(...)
@collate, inputs(...)
@combinations
@combinations_with_replacement
@files
@files (on-the-fly parameter generation)
@files_re
@follows
@graphviz
@jobs_limit
@merge
@mkdir
@originate
@parallel
@permutations
@posttask
@product
@split
@subdivide
@transform
@transform, add_inputs(...)
@transform, inputs(...)
T
t_black_hole_logger (class in ruffus.task)
t_stderr_logger (class in ruffus.task)
task
Task completion
Tutorial
Timestamp resolution
Manual
touch mode pipeline_run
Tutorial
touch_file
@posttask (Syntax)
touchfile
@posttask (Manual)
transform
Tutorial
transform_param_factory() (in module ruffus.task)
transforming in parallel
Tutorial
Tutorial
@active_if
@collate
@jobs_limit
@parallel
@subdivide
Checking dependencies
Exceptions
Interrupted Pipeline
Mixing tasks, globs and file names
Regenerating the checkpoint file
Ruffus names list
Task completion
Up to date
add_inputs
check_if_uptodate
combinatorics
command line
data sharing across processes
decorators_compendium
deprecated @files
deprecated @files_re
exceptions
flowchart colours
,
[1]
formatter
globs in input parameters
input / output parameters
inputs
interrupting tasks
logging
logging customising
logging with ruffus.cmdline
logging your own message
merge
mkdir
multiprocessing
on_the_fly
one to one @transform
originate
output file names
overview
pipeline_printout
pipeline_printout_graph
pipeline_run
pipeline_run touch mode
pipeline_run verbosity
pipeline_run(multiprocess)
posttask
regex
split
string substiution for inputs
suffix
touch mode pipeline_run
transform
transforming in parallel
Tutorial on-the-fly parameter generation
@files
U
Up to date
Tutorial
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