pepkit/looper

Issues

• looper report messaging

  #533 opened 3 months ago by nsheff
  1

• looper report happily makes an empty report

  #537 opened 4 months ago by nsheff
  0

• looper report file location parameter missing

  #534 opened 4 months ago by nsheff
  1

• Rerun documentation

  #531 opened 5 months ago by nsheff
  1

• portable report zip missing extension

  #532 opened 5 months ago by nsheff
  1

• Running a looper pipeline ad hoc

  #538 opened 4 months ago by nleroy917
  4

• looper table appears to re-create the item once per sample, and makes empty table

  #536 opened 4 months ago by nsheff
  3

• looper report makes files with spaces in names

  #535 opened 4 months ago by nsheff
  0

• Reduce verbosity of refgenie tag plugin?

  #529 opened 5 months ago by nsheff
  2

• divvy is not using the correct template directory

  #530 opened 5 months ago by nsheff
  1

• Misleading error message if pipeline_interface path does not exist

  #528 opened 5 months ago by nsheff
  0

• divvy dev suggestions

  #527 opened 5 months ago by nsheff
  0

• Run a single sample

  #526 opened 5 months ago by nleroy917
  2

• `sizing` keyword is not working correctly

  #524 opened 6 months ago by nsheff
  1

• looper is not validating inputs correctly

  #523 opened 6 months ago by nsheff
  3

• Making looper approachable for a new project

  #466 opened a year ago by nsheff
  6

• looper report runs pipestat summarize multiple times

  #522 opened 6 months ago by donaldcampbelljr
  0

• input schema fails to validate

  #521 opened 7 months ago by donaldcampbelljr
  1

• Improve error message for bad looper config

  #515 opened 7 months ago by nsheff
  6

• divvy init gives error when initializing new default

  #520 opened 7 months ago by donaldcampbelljr
  0

• Error: looper requires JWT for retrieving public PEP from PEPhub

  #516 opened 7 months ago by nsheff
  5

• looper config should allow for pipestat pephub path.

  #519 opened 7 months ago by donaldcampbelljr
  0

• looper cli is not taking priority if cli modifiers are used in looper config

  #518 opened 7 months ago by donaldcampbelljr
  3

• Make suggested changes to `looper init`

  #514 opened 7 months ago by donaldcampbelljr
  4

• Remove printed dict at looper finish

  #511 opened 7 months ago by donaldcampbelljr
  1

• divvy list error

  #512 opened 7 months ago by nsheff
  1

• Speeding up looper CLI use

  #476 opened a year ago by nsheff
  4

• how do to parallel-process files with looper locally -- lump them together, this will group several commands in one like:

  #498 opened 9 months ago by donaldcampbelljr
  1

• For Looper 2.0, we will consolidate sample and project level pipeline interfaces under a single interface.

  #493 opened 10 months ago by donaldcampbelljr
  0

• It's unclear why the pipeline type is specified both in the pipeline interface and the looper config

  #465 opened 9 months ago by nsheff
  2

• PyTestReturnNotNoneWarning

  #491 opened 9 months ago by donaldcampbelljr
  1

• Input PEP for Looper vs output PEP given to Pipestat

  #490 opened 9 months ago by donaldcampbelljr
  1

• Unclear how to configure pipestat namespace name with looper for file backend

  #460 opened 9 months ago by nsheff
  3

• KeyError: '_cli_extra' when calling looper run

  #497 opened 9 months ago by joseverdezoto
  4

• Imprecise looper documentation for getting started

  #488 opened 9 months ago by kripkd
  2

• Project name cannot be inferred when loading PEP from csv

  #484 opened 9 months ago by donaldcampbelljr
  1

• Refactor Looper's integration of Pipestat

  #492 opened 9 months ago by donaldcampbelljr
  12

• Looper runp produces `default_project_record_identifier` folder with an empty stats.yaml

  #471 opened 9 months ago by donaldcampbelljr
  2

• Looper resolves pipeline interface paths differently if multiple interfaces are supplied

  #474 opened 9 months ago by donaldcampbelljr
  0

• completed flag check may erroneously stop on regex matches

  #470 opened 9 months ago by nsheff
  6

• Does looper destroy also clear pipestat results?

  #469 opened 9 months ago by nsheff
  2

• looper rerun is not only running failed jobs, but everything

  #467 opened 9 months ago by nsheff
  1

• looper destroy is broken

  #468 opened 9 months ago by nsheff
  2

• pipestat status flags are not working correctly

  #463 opened 9 months ago by nsheff
  1

• Rethinking looper testing

  #464 opened 9 months ago by nsheff
  8

• extra pipestat message

  #461 opened 9 months ago by nsheff
  2

• looper inspect is broken

  #462 opened 9 months ago by nsheff
  3

• Strange behavior of looper check

  #459 opened 9 months ago by nsheff
  5

• Error running the CLI

  #494 opened 10 months ago by nleroy917
  2

• Appending "command_extra" for looper runp appears to be broken

  #475 opened a year ago by donaldcampbelljr
  2