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oxo-flow

clean

Traitome/oxo-flow

`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
`--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

Output#

Dry-run output#

oxo-flow 0.1.0 — 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 0.1.0 — 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

Notes#

Wildcard patterns (containing { and }) are skipped because they cannot be resolved to specific files without runtime context
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