Resume an interrupted run¶


For	Users whose run stopped or has failed/incomplete samples
Hands-on steps	Read status, inspect first log, correct cause, repeat exact command
Prerequisites	Original output and work directories; same intended inputs/settings
Download/storage	Resume can continue container/model/download work; check free space first
Writes to	Existing result/work paths, with valid cached tasks reused

Ask TumorQuantAI what happened¶

tumorquantai status /data/results-fast
tumorquantai status /data/results-fast --json > status.json

Status parses workflow metadata, per-sample summaries, and aggregated_celltypes/sample_aggregation_audit.csv. It reports completed, failed, incomplete, excluded, and pending samples, then prints:

the first relevant log to inspect; and
the exact resume command when recorded.

Human status is a local operational view and may contain exact filesystem paths. status --json and generated reports redact sensitive paths for sharing; credential locations are never recorded. Review any human terminal output before posting it.

A failed sample is not a biological zero. It remains out of the numeric matrices and visible in the audit.

Correct and resume¶

Resolve the reported environmental/input problem, then repeat the same command. Resume is enabled by default:

tumorquantai run /data/slides \
  --output /data/results-fast \
  --preset fast \
  --source-mpp "$SOURCE_MPP"

Changing the source fingerprint, L2 companion, source MPP, sampling, seed, container/model identity, or relevant settings invalidates affected cached tasks. That is a safeguard, not a resume failure.

Use --no-resume only for an intentional fresh execution. Keep the new run in a separate output/work pair when scientific settings change.

Stop and clean up¶

Press Ctrl+C to stop safely. Do not move an active work directory or run nextflow clean -f while recovery is needed. After published outputs, provenance, and audit are verified and backed up, remove only the exact work directory associated with that run.

Next: if resume still fails, open Troubleshooting.