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oxo-flow

touch

Traitome/oxo-flow

`oxo-flow touch`#

Mark workflow outputs as up-to-date without re-executing rules.

Usage#

oxo-flow touch [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option	Short	Description
`--rule`	`-r`	Specific rule(s) whose outputs to touch
`--workdir <DIR>`	`-d`	Working directory the outputs live in (default: the workflow file's directory)

Examples#

Touch all outputs#

oxo-flow touch pipeline.oxoflow

Touch outputs of a specific rule#

oxo-flow touch pipeline.oxoflow -r bwa_align

Output#

oxo-flow v0.15.0 — Rust-native bioinformatics pipeline engine
  ✓ sample1.bam
  ✓ sample1.bam.bai
  ✓ sample2.bam
  ✓ sample2.bam.bai

Done: 4 file(s) touched, 0 wildcard pattern(s) skipped

Notes#

Updates the modification time of output files to the current time
If an output file does not exist, an empty file will be created
Useful for forcing the engine to skip rules when outputs were generated externally
Wildcard patterns are skipped as they cannot be touched without specific values