Issues

• Idea: a Stage that's always rerun

  brainstormingenhancementquestion
  databio/pypiper#231 · Filter by author vreuter opened on Jan 17, 2025
  

• how to deal with huge fastq files

  question
  databio/pypiper#229 · Filter by author zhangzhen opened on Jul 23, 2024
  1

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

  bug
  databio/pypiper#228 · Filter by author vreuter opened on Jun 1, 2024
  

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

  question
  databio/pypiper#227 · Filter by author vreuter opened on Jun 1, 2024

• Pipeline "failure reason" loses some information

  databio/pypiper#226 · Filter by author vreuter opened on May 30, 2024

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

  bugpriority-low
  databio/pypiper#225 · Filter by author vreuter opened on May 17, 2024
  1

• Rerun of downstream Stages should be configurable, probably opt-in

  enhancement
  databio/pypiper#224 · Filter by author vreuter opened on May 8, 2024
  

• Add summary of Stages of Pipeline which failed

  enhancement
  databio/pypiper#221 · Filter by author vreuter opened on May 5, 2024
  

• Idea: "describe" a pipeline

  brainstormingdesignenhancementquestion
  databio/pypiper#217 · Filter by author vreuter opened on Apr 8, 2024

• Running tests locally generates (or changes?) outputs that are not .gitignored

  databio/pypiper#214 · Filter by author vreuter opened on Feb 18, 2024
  1

• Pipeline log file could collide with filepath given to logmuse

  databio/pypiper#212 · Filter by author vreuter opened on Feb 17, 2024
  2

  

• Critical bugs with reporting results

  bugpriority-high
  databio/pypiper#209 · Filter by author nsheff opened on Feb 17, 2024
  3

• docs outdated?

  docs
  databio/pypiper#208 · Filter by author nsheff opened on Feb 15, 2024
  2

• KeyError: 'Time' when using pipestat via pypiper

  databio/pypiper#207 · Filter by author nsheff opened on Feb 15, 2024
  6

• unifying pipestat config with pipestat constructor

  enhancement
  databio/pypiper#206 · Filter by author nsheff opened on Feb 15, 2024
  2

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

  bugpriority-high
  databio/pypiper#205 · Filter by author donaldcampbelljr opened on Feb 14, 2024
  4

• report_result docstrings for value is inaccurate

  databio/pypiper#204 · Filter by author donaldcampbelljr opened on Feb 13, 2024
  2

• DeprecationWarning for many regex patterns / escape sequences

  databio/pypiper#203 · Filter by author vreuter opened on Dec 28, 2023

• Test assertions should use constant for default sample name

  tests
  databio/pypiper#194 · Filter by author vreuter opened on Jul 7, 2023

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

  bug
  databio/pypiper#193 · Filter by author vreuter opened on Jul 7, 2023

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

  brainstormingbug
  databio/pypiper#192 · Filter by author vreuter opened on Jul 7, 2023
  1

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

  bugdocs
  databio/pypiper#191 · Filter by author vreuter opened on Jul 6, 2023
  1

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

  databio/pypiper#189 · Filter by author zhangzhen opened on Jun 18, 2023
  4

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

  databio/pypiper#186 · Filter by author donaldcampbelljr opened on Jun 13, 2023

• Tests should clean up after running

  databio/pypiper#185 · Filter by author donaldcampbelljr opened on Jun 12, 2023
  3