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oxo-flow clean#

Clean workflow outputs and temporary files. Removes files declared as outputs in the workflow's rules.

Usage#

oxo-flow clean [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option Short Default Description
--dry-run -n — Show what would be cleaned without deleting
--force — — Skip the confirmation prompt
--orphans — — Clean orphaned temporary files (chunks from interrupted transforms)
--verbose -v — Enable debug-level logging

Examples#

Preview what would be cleaned#

oxo-flow clean pipeline.oxoflow -n

Clean with confirmation prompt#

oxo-flow clean pipeline.oxoflow

Clean without confirmation#

oxo-flow clean pipeline.oxoflow --force

Clean orphaned chunks from interrupted transforms#

# When a transform operation is interrupted (Ctrl+C), chunk files
# may remain in .oxo-flow/chunks/. Use --orphans to clean them.
oxo-flow clean pipeline.oxoflow --orphans

Output#

Dry-run output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
Would clean (dry-run):
  results/trimmed/sample1_R1.fastq.gz (exists)
  results/trimmed/sample1_R2.fastq.gz (exists)
  results/aligned/{sample}.bam (wildcard, skipped)
  results/report.html (not found)

Total: 4 output patterns

Clean output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
Clean: 2 file(s) will be deleted. Continue? [y/N]
y
  ✓ results/trimmed/sample1_R1.fastq.gz
  ✓ results/trimmed/sample1_R2.fastq.gz

Done: 2 deleted, 0 failed, 1 not found, 1 wildcard skipped, 0 rejected

Notes#

  • Wildcard patterns (containing { and }) are skipped because they cannot be resolved to specific files without runtime context
  • Path Traversal Protection strictly rejects paths that begin with /, ~, or contain .., marking them as rejected and preventing arbitrary file deletion
  • Non-existent files are silently skipped (not counted as errors)
  • Without --force, a confirmation prompt is shown before deleting any files
  • Use --dry-run to preview the list of files that would be affected before committing to a clean
  • Only files declared as rule output are targeted — input files, scripts, and environment specs are never deleted