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Add support for CellRanger ARC#15

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arteymix wants to merge 55 commits intomasterfrom
feature-cellranger-arc
Draft

Add support for CellRanger ARC#15
arteymix wants to merge 55 commits intomasterfrom
feature-cellranger-arc

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arteymix and others added 30 commits October 21, 2025 18:48
Eliminate RemoveTaskOutputOnFailureMixin.
Move schedulers in a new module and add an interface for schedulable
tasks.

Include Luigi metadata in the Slurm --comment field.
arteymix and others added 25 commits October 22, 2025 10:36
Task parameters can be overwritten by the subclass, so it's best to
defer their validation when they are actually used.
Make srun binary configurable

Add individual configuration sections for each scheduler.

Add a test configuration to use for the CI.
Simply use the task ID in the comment instead of nesting a JSON payload.

Cache squeue output to minimize the number of calls to squeue,
especially when multiple workers are overseeing Slurm jobs.

Peform more validation with graceful logging when the squeue payload
does not match expectations.
Use a patched LocalTarget for every tasks.
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