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* add failing tests 823 * fix mistakes * black * Update tests from #823 MREs - Can't have the b.txt in first text be temp and expect it present, it will correctly be deleted. - Add third MRE which is targeting more of a log issue * Add error message printed if #823 is encountered, also exit 1 The main scheduler loop terminates if there are no more runnable jobs. This tests if there still are jobs that should be run, but that we cannot seem to get to. If so, print an error message, print the files affected, and exit 1. The latter is important so Snakemake can, as hotfix, be rerun in a loop until it's actually completed all tasks. * Fix checkpoint+temp leads to incomplete run issue The aggressive early deletion of temp files must ignore checkpoints. Other rules depend on a checkpoint only via the first output file of the checkpoint (flagged string) as a stub. All other outputs marked as temp would be deleted (and have been before this patch). Since those files are missing, the dependent rules will never be runnable and the workflow ends before all targets have been built. * Don't break untiljobs * fix typo Co-authored-by: Maarten-vd-Sande <firstname.lastname@example.org> Co-authored-by: Johannes Köster <email@example.com> Co-authored-by: Johannes Köster <firstname.lastname@example.org>
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