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cellranger_count.py: remove any existing output directory #315

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nick-youngblut opened this issue Apr 9, 2024 · 3 comments
Open

cellranger_count.py: remove any existing output directory #315

nick-youngblut opened this issue Apr 9, 2024 · 3 comments
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enhancement New feature or request

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@nick-youngblut
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Description of feature

For the sake of debugging failed CELLRANGER_COUNT processes, it would be helpful if cellranger_count.py removed any existing output directory so that .command.run can be run multiple times without having to delete the output directory in between each run (otherwise, you get the error RuntimeError: pipestance 'OUTPUT_DIRECTORY' already exists).

@nick-youngblut nick-youngblut added the enhancement New feature or request label Apr 9, 2024
@grst
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grst commented Apr 10, 2024

Don't have any objections, but why would you need to do that? If a process fails it should start in a new work directory the next time.

@nick-youngblut
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For debugging: going to that working directory and re-running the job (bash .command.run).
Definitely just a nice-to-have.

@grst
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grst commented Apr 11, 2024

Feel free to submit a PR to the modules repo!

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