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databio / pypiper

Python toolkit for building restartable pipelines
http://pypiper.databio.org
BSD 2-Clause "Simplified" License
45 stars 9 forks source link

Setting the pipeline folder to a path that's not absolute causes problem for checkpointing #225

Open vreuter opened 3 months ago

vreuter commented 3 months ago

When using a Pipeline and configuring the outfolder with a value that's not an absolute path causes the checkpoint call to fail due to trying to write to a file in a subfolder of the same name, e.g. "pypiper_output" --> Path.cwd() / "pypiper_output" / "pypiper_output" / "my_stage.checkpoint" instead of Path.cwd() / "pypiper_output" / "my_stage.checkpoint"

vreuter commented 3 months ago

Marking as low-priority since this can be readily worked around by passing an absolute path