Index

Symbols | A | B | C | D | E | F | G | I | J | L | M | N | O | P | R | S | T

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Symbols

@check_if_uptodate Manual Syntax @collate Manual Syntax @collate (Advanced Usage) Syntax @collate, add_inputs(...) Syntax @collate, inputs(...) Syntax @files Manual Syntax Tutorial Tutorial on-the-fly parameter generation check if up to date in parallel @files (on-the-fly parameter generation) Syntax @files_re Manual Syntax combine (Deprecated Syntax) @follows Manual Syntax mkdir (Manual) mkdir (Syntax) multiple dependencies out of order referring to functions before they are defined @jobs_limit Manual Syntax @merge Manual Syntax Tutorial

@parallel Manual Syntax @posttask Manual Syntax Tutorial touch_file (Syntax) touchfile (Manual) touchfile (Tutorial) @split Manual Syntax Tutorial @split (Advanced Usage) Syntax @split, add_inputs Syntax @split, inputs Syntax @split, regex Syntax @transform Manual Syntax Tutorial @transform (Advanced Usage) Manual @transform, add_inputs(...) Syntax @transform, inputs(...) Syntax

A

Acknowledgements add_inputs Indicator Object (Adding additional input parameters) args_param_factory() (in module ruffus.task)

as input parameters (Manual) tasks

B

break, [1]

C

check if up to date @files collate_param_factory() (in module ruffus.task) combine @follows (Deprecated Syntax) Manual combined with globs and files as input parameters (Manual) tasks

combined with tasks and files as input parameters (Manual) globs Comparison of Ruffus with alternatives Design

D

Debugging Manual decorator decorators Manual Tutorial

dependencies Manual Design Comparison of Ruffus with alternatives Ruffus

E

errors, [1] Etymology Ruffus Exception Missing input files

Exceptions Manual exceptions, [1]

F

files_param_factory() (in module ruffus.task) files_re_param_factory() (in module ruffus.task) for rerunning jobs rules

G

generator globs combined with tasks and files as input parameters (Manual) inputs parameters globs combined with tasks and files as input parameters Manual

globs in input parameters Manual

I

importing ruffus in parallel @files Indicator Object (Adding additional input parameters) add_inputs Indicator Object (Disambiguating parameters) combine mkdir output_from regex suffix touch_file Indicator Object (Replacing input parameters) inputs

input / output parameters Tutorial inputs Indicator Object (Replacing input parameters) inputs / outputs parameters Manual inputs parameters globs refering to tasks by name tasks interrupts, [1] introduction manual

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 Manual

M

make_shared_logger_and_proxy() (in module ruffus.proxy_logger) manual introduction Manual @check_if_uptodate @collate @files @files_re @follows @jobs_limit @merge @parallel @posttask @split @transform @transform (Advanced Usage) Debugging Exceptions Logging Running the pipeline Tracing pipeline parameters combine decorators dependencies globs combined with tasks and files as input parameters globs in input parameters inputs / outputs parameters pipeline_printout, [1] pipeline_printout_graph pipeline_run, [1] skip up-to-date tasks as input parameters tasks as recipes, [1] tasks combined with globs and files as input parameters

merge_param_factory() (in module ruffus.task) Missing input files Exception mkdir @follows (Manual) @follows (Syntax) multiple dependencies @follows multiple errors

N

Name origins Ruffus needs_update_check_directory_missing() (in module ruffus.task)

needs_update_check_modify_time() (in module ruffus.task)

O

out of order @follows output_from Indicator Object (Disambiguating parameters)

P

pipeline functions pipeline_printout_graph pipeline_run, [1] pipeline_printout Manual, [1] Printout simulated run of the pipeline Tutorial, [1] pipeline_printout() (in module ruffus.task) pipeline_printout_graph Manual Tutorial print flowchart representation of pipeline functions

pipeline_printout_graph() (in module ruffus.task) pipeline_run Manual, [1] Run pipeline Tutorial pipeline_run() (in module ruffus.task) print flowchart representation of pipeline functions pipeline_printout_graph Printout simulated run of the pipeline pipeline_printout

R

refering to by name tasks refering to tasks by name inputs parameters referring to functions before they are defined @follows regex Indicator Object (Disambiguating parameters) Ruffus Design Etymology Name origins

ruffus.proxy_logger (module) rules for rerunning jobs Run pipeline pipeline_run Running the pipeline Manual

S

setup_std_shared_logger() (in module ruffus.proxy_logger) signalling, [1] skip up-to-date Manual split_param_factory() (in module ruffus.task) suffix Indicator Object (Disambiguating parameters) Syntax @check_if_uptodate @collate @collate (Advanced Usage) @collate, add_inputs(...) @collate, inputs(...) @files @files (on-the-fly parameter generation) @files_re @follows @jobs_limit @merge @parallel @posttask @split @split (Advanced Usage) @split, add_inputs @split, inputs @split, regex @transform @transform, add_inputs(...) @transform, inputs(...)

T

t_black_hole_logger (class in ruffus.task) t_stderr_logger (class in ruffus.task) task tasks as input parameters (Manual) combined with globs and files as input parameters (Manual) inputs parameters refering to by name tasks as input parameters Manual tasks as recipes Manual, [1] tasks combined with globs and files as input parameters Manual Timestamp resolution touch_file @posttask (Syntax) touchfile @posttask (Manual) @posttask (Tutorial)

Tracing pipeline parameters Manual transform_param_factory() (in module ruffus.task) Tutorial @files @merge @posttask @split @transform decorators input / output parameters pipeline_printout, [1] pipeline_printout_graph pipeline_run Tutorial on-the-fly parameter generation @files