Resume behavior

A re-run skips too many steps

Steps skip themselves when their outputs already exist. Delete the stale outputs, or PoolSeqFlow reset to start over.

A re-run submits every job anyway

Expected. Step-skipping happens inside each task rather than before it, so a fully resumed run still submits roughly one short job per process per sample. Resume Logic →

-resume appears to do nothing

Correct. PoolSeqFlow does not use Nextflow's -resume, and the wrapper never passes it. PoolSeqFlow run already resumes. Resume Logic ->

A step reruns after an interrupted job

If the interruption hit a cross-filesystem move, the partial copy was left under a temporary name rather than under the final one, so the step correctly runs again. That is the atomic move working.