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55 Open 113 Closed
55 Open 113 Closed
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Issues list

how to deal with huge fastq files question
#229 opened Jul 23, 2024 by zhangzhen
1
Pipeline doesn't respect -N / --new-start bug
#228 opened Jun 1, 2024 by vreuter
@vreuter
Could -N / --new-start be given an alias, like --clobber or --overwrite? question
#227 opened Jun 1, 2024 by vreuter
Pipeline "failure reason" loses some information
#226 opened May 30, 2024 by vreuter
Setting the pipeline folder to a path that's not absolute causes problem for checkpointing bug priority-low
#225 opened May 17, 2024 by vreuter
1
Rerun of downstream Stages should be configurable, probably opt-in enhancement
#224 opened May 8, 2024 by vreuter
@vreuter
Add summary of Stages of Pipeline which failed enhancement
#221 opened May 5, 2024 by vreuter
@vreuter
Idea: "describe" a pipeline brainstorming design enhancement question
#217 opened Apr 8, 2024 by vreuter
Running tests locally generates (or changes?) outputs that are not .gitignored
#214 opened Feb 18, 2024 by vreuter
1
Pipeline log file could collide with filepath given to logmuse
#212 opened Feb 17, 2024 by vreuter
1
@vreuter
2
Critical bugs with reporting results bug priority-high
#209 opened Feb 17, 2024 by nsheff
3
docs outdated? docs
#208 opened Feb 15, 2024 by nsheff
2
KeyError: 'Time' when using pipestat via pypiper
#207 opened Feb 15, 2024 by nsheff
6
unifying pipestat config with pipestat constructor enhancement
#206 opened Feb 15, 2024 by nsheff
@donaldcampbelljr
2
multi=False causes Errno 29 illegal seek during pytest teardown bug priority-high
#205 opened Feb 14, 2024 by donaldcampbelljr
4
report_result docstrings for value is inaccurate
#204 opened Feb 13, 2024 by donaldcampbelljr
2
DeprecationWarning for many regex patterns / escape sequences
#203 opened Dec 28, 2023 by vreuter
Test assertions should use constant for default sample name tests
#194 opened Jul 7, 2023 by vreuter
"start-point" is not included in the "checkpoint" group bug
#193 opened Jul 7, 2023 by vreuter
In minimal use case, add_pypiper_args fails when composed with logmuse.add_logging_options brainstorming bug
#192 opened Jul 7, 2023 by vreuter
1
Documentation of the key method to implement to create a Pipeline type is wrong bug docs
#191 opened Jul 6, 2023 by vreuter
1
Can Pypiper generate a DAG to guide the execution of commands that comprise a pipeline?
#189 opened Jun 18, 2023 by zhangzhen
4
During testing, logging errors are generated: "ValueError: I/O operation on closed file"
#186 opened Jun 13, 2023 by donaldcampbelljr
Tests should clean up after running
#185 opened Jun 12, 2023 by donaldcampbelljr
3
AttributeError: module 'pypiper' has no attribute 'add_pypiper_args'
#183 opened Feb 16, 2023 by wilfriedguiblet
2
ProTip! Updated in the last three days: updated:>2024-12-18.