databio/pypiper

Issues

• how to deal with huge fastq files

  #229 opened 4 months ago by zhangzhen
  1

• `Pipeline` doesn't respect `-N` / `--new-start`

  #228 opened 6 months ago by vreuter
  0

• Could `-N` / `--new-start` be given an alias, like `--clobber` or `--overwrite`?

  #227 opened 6 months ago by vreuter
  0

• Pipeline "failure reason" loses some information

  #226 opened 6 months ago by vreuter
  0

• Setting the pipeline folder to a path that's not absolute causes problem for checkpointing

  #225 opened 6 months ago by vreuter
  1

• `logger_kwargs` isn't used in one branch of the pipeline manager setup

  #211 opened 7 months ago by vreuter
  4

• Add summary of `Stage`s of `Pipeline` which failed

  #221 opened 7 months ago by vreuter
  0

• Rerun of downstream `Stage`s should be configurable, probably opt-in

  #224 opened 7 months ago by vreuter
  0

• Add `nofail` to `Stage`

  #218 opened 7 months ago by vreuter
  0

• Critical bugs with reporting results

  #209 opened 9 months ago by nsheff
  3

• Replace read_yaml_data with yacman.load_yaml

  #216 opened 7 months ago by donaldcampbelljr
  1

• `pipestat_project_name` parameter to manager constructor is currently unused

  #213 opened 7 months ago by vreuter
  3

• Idea: "describe" a pipeline

  #217 opened 8 months ago by vreuter
  0

• multi=False causes Errno 29 illegal seek during pytest teardown

  #205 opened 9 months ago by donaldcampbelljr
  4

• Running tests locally generates (or changes?) outputs that are not `.gitignore`d

  #214 opened 9 months ago by vreuter
  1

• Pipeline log file could collide with filepath given to logmuse

  #212 opened 9 months ago by vreuter
  2

• Logs are overwritten with new pipeline run

  #210 opened 9 months ago by nsheff
  6

• docs outdated?

  #208 opened 9 months ago by nsheff
  2

• KeyError: 'Time' when using pipestat via pypiper

  #207 opened 9 months ago by nsheff
  6

• unifying pipestat config with pipestat constructor

  #206 opened 9 months ago by nsheff
  2

• report_result docstrings for value is inaccurate

  #204 opened 9 months ago by donaldcampbelljr
  2

• Pypiper should support `force_overwrite` when reporting results?

  #201 opened 9 months ago by donaldcampbelljr
  1

• `DeprecationWarning` for many regex patterns / escape sequences

  #203 opened a year ago by vreuter
  0

• Initial logging message about a stage is a bit odd

  #197 opened a year ago by vreuter
  0

• SyntaxWarning on first import

  #196 opened a year ago by vreuter
  1

• get_stat should use pipestat's retrieve_one

  #202 opened a year ago by donaldcampbelljr
  1

• Overwrite checkpoints when new start is active

  #174 opened a year ago by vreuter
  1

• Should we remove checkpointing functionality?

  #184 opened a year ago by nsheff
  2

• Tests should clean up after running

  #185 opened a year ago by donaldcampbelljr
  3

• In minimal use case, add_pypiper_args fails when composed with logmuse.add_logging_options

  #192 opened a year ago by vreuter
  1

• Can Pypiper generate a DAG to guide the execution of commands that comprise a pipeline?

  #189 opened a year ago by zhangzhen
  4

• Test assertions should use constant for default sample name

  #194 opened a year ago by vreuter
  0

• "start-point" is not included in the "checkpoint" group

  #193 opened a year ago by vreuter
  0

• Documentation of the key method to implement to create a Pipeline type is wrong

  #191 opened a year ago by vreuter
  1

• Pypiper should utilize pipestat to report results

  #187 opened a year ago by donaldcampbelljr
  1

• Package name is case-sensitive for import?

  #190 opened a year ago by vreuter
  1

• During testing, logging errors are generated: "ValueError: I/O operation on closed file"

  #186 opened a year ago by donaldcampbelljr
  0

• AttributeError: module 'pypiper' has no attribute 'add_pypiper_args'

  #183 opened 2 years ago by wilfriedguiblet
  2

• Are there any better tutorials that what is present on the pypiper website?

  #168 opened 2 years ago by Rob-murphys
  4

• pypiper args not being picked up

  #176 opened 2 years ago by vreuter
  1

• Python >= 3.9 breaks the ability to treat .keys() as a list for concatenation.

  #178 opened 3 years ago by jpsmith5
  1

• Python 3 changes the type of filter() from a list like object to an iterator.

  #179 opened 3 years ago by jpsmith5
  1

• Python 3.10 error on importing from collections

  #182 opened 3 years ago by nsheff
  0

• Consider removing -R?

  #173 opened 4 years ago by vreuter
  4

• Docker feature doesn't work on macOS

  #172 opened 4 years ago by nsheff
  1

• compressed output

  #171 opened 5 years ago by nsheff
  0

• Rename 'total elapsed time'

  #170 opened 5 years ago by stolarczyk
  0

• python 3 err

  #166 opened 5 years ago by nsheff
  1

• time accumulation from profile is inaccurate

  #165 opened 5 years ago by nsheff
  6

• initialize profile only after first cmd

  #164 opened 5 years ago by nsheff
  1