Index

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