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databio
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pypiper
Python toolkit for building restartable pipelines
http://pypiper.databio.org
BSD 2-Clause "Simplified" License
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how to deal with huge fastq files
#229
zhangzhen
opened
1 week ago
1
`Pipeline` doesn't respect `-N` / `--new-start`
#228
vreuter
opened
2 months ago
0
Could `-N` / `--new-start` be given an alias, like `--clobber` or `--overwrite`?
#227
vreuter
opened
2 months ago
0
Pipeline "failure reason" loses some information
#226
vreuter
opened
2 months ago
0
Setting the pipeline folder to a path that's not absolute causes problem for checkpointing
#225
vreuter
opened
2 months ago
1
Rerun of downstream `Stage`s should be configurable, probably opt-in
#224
vreuter
opened
2 months ago
0
v0.14.2 release
#223
donaldcampbelljr
closed
2 months ago
1
Don't checkpoint a nofail stage when it's nofailed
#222
vreuter
closed
2 months ago
0
Add summary of `Stage`s of `Pipeline` which failed
#221
vreuter
opened
3 months ago
0
Give `Stage` the `nofail` behavior option
#220
vreuter
closed
2 months ago
4
v0.14.1 release
#219
donaldcampbelljr
closed
3 months ago
0
Add `nofail` to `Stage`
#218
vreuter
closed
2 months ago
0
Idea: "describe" a pipeline
#217
vreuter
opened
3 months ago
0
Replace read_yaml_data with yacman.load_yaml
#216
donaldcampbelljr
closed
3 months ago
1
Check that logfile for manager's logger doesn't collide with manager's own logfile
#215
vreuter
closed
5 months ago
12
Running tests locally generates (or changes?) outputs that are not `.gitignore`d
#214
vreuter
opened
5 months ago
1
`pipestat_project_name` parameter to manager constructor is currently unused
#213
vreuter
closed
3 months ago
3
Pipeline log file could collide with filepath given to logmuse
#212
vreuter
opened
5 months ago
2
`logger_kwargs` isn't used in one branch of the pipeline manager setup
#211
vreuter
closed
2 months ago
4
Logs are overwritten with new pipeline run
#210
nsheff
closed
5 months ago
6
Critical bugs with reporting results
#209
nsheff
opened
5 months ago
3
docs outdated?
#208
nsheff
opened
5 months ago
2
KeyError: 'Time' when using pipestat via pypiper
#207
nsheff
opened
5 months ago
6
unifying pipestat config with pipestat constructor
#206
nsheff
opened
5 months ago
2
multi=False causes Errno 29 illegal seek during pytest teardown
#205
donaldcampbelljr
opened
5 months ago
4
report_result docstrings for value is inaccurate
#204
donaldcampbelljr
opened
5 months ago
2
`DeprecationWarning` for many regex patterns / escape sequences
#203
vreuter
opened
7 months ago
0
get_stat should use pipestat's retrieve_one
#202
donaldcampbelljr
closed
8 months ago
1
Pypiper should support `force_overwrite` when reporting results?
#201
donaldcampbelljr
closed
5 months ago
1
0.14.0 Release
#200
donaldcampbelljr
closed
7 months ago
1
updated to pipestat 0.6.0
#199
khoroshevskyi
closed
8 months ago
0
Cleaner initial stage run message
#198
vreuter
closed
9 months ago
0
Initial logging message about a stage is a bit odd
#197
vreuter
closed
7 months ago
0
SyntaxWarning on first import
#196
vreuter
closed
7 months ago
1
Add _safe_write_to_file back to pypiper for Pepatac backwards compat
#195
donaldcampbelljr
closed
1 year ago
0
Test assertions should use constant for default sample name
#194
vreuter
opened
1 year ago
0
"start-point" is not included in the "checkpoint" group
#193
vreuter
opened
1 year ago
0
In minimal use case, add_pypiper_args fails when composed with logmuse.add_logging_options
#192
vreuter
opened
1 year ago
1
Documentation of the key method to implement to create a Pipeline type is wrong
#191
vreuter
opened
1 year ago
1
Package name is case-sensitive for import?
#190
vreuter
closed
1 year ago
1
Can Pypiper generate a DAG to guide the execution of commands that comprise a pipeline?
#189
zhangzhen
opened
1 year ago
4
Pipestat addition
#188
donaldcampbelljr
closed
1 year ago
7
Pypiper should utilize pipestat to report results
#187
donaldcampbelljr
closed
1 year ago
1
During testing, logging errors are generated: "ValueError: I/O operation on closed file"
#186
donaldcampbelljr
opened
1 year ago
0
Tests should clean up after running
#185
donaldcampbelljr
opened
1 year ago
3
Should we remove checkpointing functionality?
#184
nsheff
closed
1 year ago
2
AttributeError: module 'pypiper' has no attribute 'add_pypiper_args'
#183
wilfriedguiblet
opened
1 year ago
2
Python 3.10 error on importing from collections
#182
nsheff
closed
2 years ago
0
Hotfix 0.12.3
#181
nsheff
closed
2 years ago
0
Release 0.13.0
#180
nsheff
closed
1 year ago
1
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