fix: fix premature deletion of temp files in combination with checkpoints#2737
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johanneskoester merged 1 commit intomainfrom Mar 7, 2024
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fix: fix premature deletion of temp files in combination with checkpoints#2737johanneskoester merged 1 commit intomainfrom
johanneskoester merged 1 commit intomainfrom
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johanneskoester
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Mar 11, 2024
🤖 I have created a release *beep* *boop* --- ## [8.6.0](v8.5.5...v8.6.0) (2024-03-11) ### Features * add setting for defining separate local storage prefix for remote jobs; improved ergonomics for semantic helper functions ([#2743](#2743)) ([5007e5c](5007e5c)) * allow passing of lists of functions or single functions to expand ([#2741](#2741)) ([32e65df](32e65df)) ### Bug Fixes * fix error message for invalid storage provider queries ([977951e](977951e)) * fix premature deletion of temp files in combination with checkpoints ([#2737](#2737)) ([b22ba5f](b22ba5f)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
mhulsman
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Snakemake can only ensure that temp files will not be needed anymore after all checkpoint jobs have been executed (snakemake#609, snakemake#2732, fixed in snakemake#2737). However, waiting for all checkpoint jobs to be completed can lead to excessive storage use (snakemake#2982). In most cases temp file usage is either unaffected by checkpoint jobs, or can be explicitly managed by including the temp files as input to checkpoint jobs or their downstream dependencies. This will ensure they are kept on disk until they (might) be needed. To address cases where pipelines using checkpoints become infeasible due to high storage demands, this commit introduces a new command-line option. This option lets Snakemake know that it can safely remove temporary files not required by current jobs, even if checkpoint jobs are still pending.
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fixes #2732
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).