oxo-flow status

Show execution status from a checkpoint file. Displays which rules completed successfully and which failed.

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Usage

oxo-flow status <CHECKPOINT>

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Arguments

Argument	Description
<CHECKPOINT>	Path to a checkpoint JSON file (e.g., .oxo-flow/checkpoint.json)

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Options

Option	Short	Description
--verbose	-v	Enable debug-level logging

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Examples

oxo-flow status .oxo-flow/checkpoint.json

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Output

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
Checkpoint Status:
  ✓ trim_reads
  ✓ align
  ✓ sort_bam
  ✗ mark_duplicates

Summary: 3 completed, 1 failed

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Checkpoint File Format

The checkpoint file is JSON with the following structure:

{
  "completed_rules": ["trim_reads", "align", "sort_bam"],
  "failed_rules": ["mark_duplicates"],
  "benchmarks": {
    "trim_reads": {
      "rule": "trim_reads",
      "wall_time_secs": 42.5,
      "max_memory_mb": 1024,
      "cpu_seconds": 38.2
    }
  }
}

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Notes

• Checkpoint files are written automatically during oxo-flow run execution
• Use status to inspect progress of long-running pipelines, especially on clusters
• The checkpoint file is not updated after the pipeline completes — it reflects the state at the last write
• Exits with code 0 regardless of the pipeline's success or failure