AlexTate

Adding new choice to --on-error

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### Summary This pull request introduces a new choice, `kill`, for the `--on-error` parameter. ### Motivation There currently isn't a way to have cwltool immediately stop parallel jobs when one...

Continuation of #2003 ## Expected Behavior Scatter outputs should be collected only once for each scatter job. ## Actual Behavior The patch provided by @GlassOfWhiskey in PR #2051 has done...

`k2 build` deadlocks on Popen.stdin.write()

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## Environment - Ubuntu 22.04.5 - Kraken2 version 2.1.6 via Bioconda - Command: `k2 build --db DB --threads 48 --masker-threads 32 --log db_build_8.11.2025.txt` - Fresh build (no prior build outputs...

`k2 build` hangs during final steps due to total_sequences disagreement

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## Environment - Ubuntu 22.04.5 - Kraken2 version 2.1.6 via Bioconda - Command: `k2 build --db DB --threads 32 --masker-threads 16` - Fresh custom build (no prior build outputs in...

## Environment - Ubuntu 22.04.5 - Kraken2 version 2.1.6 via Bioconda - Command: `k2 add-to-library --db DB --file genome.fa` ## Behaviors Observed - Corresponding prelim_map_*.txt output file is zero bytes...