cgat-developers ruffus issues

cgat-developers / ruffus

CGAT-ruffus is a lightweight python module for running computational pipelines

MIT License

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issues

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Unable to reuse pipeline names

#78 rulai-huajunzeng opened 8 years ago
1
From one task with multiple output to many tasks with single output

#77 felixeye opened 8 years ago
0
run task function with different parameter

#76 Jerry-Ma opened 8 years ago
0
Resubmit SGE jobs up to a certain limit

#75 vasisht closed 6 years ago
1
Use job_name as prefix for job script file

#74 vasisht closed 6 years ago
1
ruffus cmdline and OO syntax

#73 mbiokyle29 opened 8 years ago
1
how to change default working dir?

#72 swuecho opened 8 years ago
0
Exception handling in task.py

#71 kemaleren opened 8 years ago
0
Duplicate task name error when using Spyder IDE

#70 msdayton opened 8 years ago
1
Small regex typo fix

#69 khughitt closed 8 years ago
0
How to collate a mixed list of file

#68 mbiokyle29 closed 8 years ago
1
Add test case to demonstrate exception on pickling RethrownJobError

#67 jbarlow83 closed 8 years ago
3
Argument parsing error messages are unhelpful

#66 bunbun opened 8 years ago
1
ruffus sometimes throws exceptions in RethrownJobError

#65 jbarlow83 closed 8 years ago
8
removal of meaningless condition & concise mkdir task names

#64 zyxue closed 6 years ago
1
OperationalError: database is locked

#63 AHCChan closed 6 years ago
2
Possible enhancement: @zipper

#62 mfalda closed 9 years ago
6
bug: drmaa_wrapper should use logger.warning instead of logger.warn

#61 bjpop closed 9 years ago
2
Improve warning about unmatched file names

#60 ghost opened 9 years ago
0
Correct error message when drmaa job exits with non-zero status.

#59 bjpop opened 9 years ago
5
Formatter sometimes resolves to different (wrong) output

#58 jrderuiter opened 9 years ago
4
Support callable objects instead of functions as tasks

#57 jrderuiter opened 9 years ago
0
Circumvent custom required args when ruffus.cmdline args are set

#56 mbiokyle29 closed 9 years ago
3
Supplying extras as a dict

#55 jrderuiter opened 9 years ago
3
active_if appears not to be respected

#54 srsridharan closed 9 years ago
1
Bug: @check_if_uptodate is ignored with @parallel

#53 bunbun closed 9 years ago
2
Zero intermediate files as soon as they are no longer necessary (posttask?)

#52 jrderuiter opened 9 years ago
1
Make command line help (especially --flowchart_format) show the default values of arguments where possible

#51 bjpop closed 9 years ago
1
Exclude non-pickable arguments from checkpointing

#50 ghost opened 9 years ago
1
Unit tests fail for 2.6.3 in Python3.2

#49 ghost opened 9 years ago
5
New Object-Orientated style syntax and ruffus.cmdline

#48 bunbun closed 9 years ago
2
Add testing code coverage

#47 bunbun opened 9 years ago
0
Python3 text/binary error in drmaa_wrapper

#46 ghost closed 9 years ago
3
substitution for extras should ignore unknowns

#45 ghost closed 9 years ago
6
Use env in drmaa.wrapper.run_job_locally

#44 ghost closed 9 years ago
4
@transform(...,suffix(...), output_dir = "xxx") only works when there is a single output file

#43 bunbun closed 9 years ago
1
output_dir parameter for more decorators

#42 ghost closed 9 years ago
1
Fix handling of various unsuccessful terminations from DRMAA.

#41 alecw closed 9 years ago
0
Python3 - pipeline_printout_graph

#40 bunbun closed 9 years ago
4
@split and @subdivide not computing output files correctly

#39 bunbun closed 9 years ago
4
Allow checkpoint files to be moved

#38 bunbun opened 9 years ago
0
@recombine

#37 bunbun opened 9 years ago
0
pipeline_printout_graph should print inactive tasks

#36 bunbun opened 9 years ago
0
decorator docs should point to manual

#35 bunbun closed 9 years ago
0
Named parameters for clarity

#34 bunbun closed 9 years ago
1
@retry_on_error(NUM_OF_RETRIES)

#33 bunbun opened 9 years ago
0
Depth first execution of Ruffus

#32 bunbun opened 9 years ago
0
Tag invocations of pipeline_run

#31 bunbun opened 9 years ago
0
Let @split returns the names of output files created rather than via "globs"

#30 bunbun opened 9 years ago
2
Cleanup created files

#29 bunbun opened 9 years ago
1

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