oxo-flow run

Execute a workflow.

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Usage

oxo-flow run [OPTIONS] <WORKFLOW>

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Arguments

Argument	Description
<WORKFLOW>	Path to the .oxoflow workflow file

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Options

Option	Short	Default	Description
--jobs	-j	1	Maximum number of concurrent jobs
--keep-going	-k	—	Continue execution when a job fails
--workdir	-d	Current directory	Working directory for execution
--target	-t	All rules	Run only specific target rules
--retry	-r	0	Number of times to retry failed jobs
--timeout	—	0 (disabled)	Timeout per job in seconds
--verbose	-v	—	Enable debug-level logging

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Examples

Run with default settings

oxo-flow run pipeline.oxoflow

Parallel execution

oxo-flow run pipeline.oxoflow -j 8

Keep going on failure

oxo-flow run pipeline.oxoflow -j 4 -k

Retry failed jobs

oxo-flow run pipeline.oxoflow -j 8 -r 2

Run specific targets

oxo-flow run pipeline.oxoflow -t align -t sort

Set a per-job timeout

oxo-flow run pipeline.oxoflow --timeout 3600

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Output

oxo-flow 0.1.0 — Bioinformatics Pipeline Engine
DAG: 5 rules in execution order
  1. fastqc
  2. trim_reads
  3. bwa_align
  4. sort_bam
  5. call_variants
  ✓ fastqc
  ✓ trim_reads
  ✓ bwa_align
  ✓ sort_bam
  ✓ call_variants

Done: 5 succeeded, 0 failed

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Notes

• The DAG is built and validated before any rules execute
• Rules are executed in topological order; independent rules may run in parallel up to the -j limit
• If --keep-going is not set, execution stops at the first failure
• The --retry flag re-runs failed jobs up to N times before marking them as failed
• A timeout of 0 means no timeout