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oxo-flow dry-run#

Simulate execution without running any commands. Shows the execution plan, rule order, and expanded shell commands.

Usage#

oxo-flow dry-run [OPTIONS] [WORKFLOW]

Arguments#

Argument Description
[WORKFLOW] Path to the .oxoflow workflow file. Optional — if not specified, auto-discovery searches for: (1) main.oxoflow in current directory, (2) alphabetically first *.oxoflow file in current directory.

Options#

Option Short Description
--target -t Preview only specific target rules and their dependencies (repeatable)
--verbose -v Enable debug-level logging

Examples#

Preview with auto-discovery#

# Auto-discover workflow in current directory
oxo-flow dry-run

Preview a specific workflow#

oxo-flow dry-run pipeline.oxoflow

Preview a specific target rule and its dependencies#

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

Preview multiple target rules#

oxo-flow dry-run pipeline.oxoflow -t align -t sort_bam

With verbose output#

oxo-flow dry-run pipeline.oxoflow -v

Output#

oxo-flow 0.6.1 — Bioinformatics Pipeline Engine
Dry-run: 3 rules would execute:
  1. trim_reads [threads=4, env=conda]
     $ fastp --in1 raw/sample1_R1.fastq.gz --in2 raw/sample1_R2.fastq.gz --out1
  2. align [threads=16, env=docker]
     $ bwa mem -t 16 /data/ref/hg38.fa trimmed/sample1_R1.fastq.gz | samtools so
  3. sort_bam [threads=4, env=conda]
     $ samtools sort -@ 4 -o sorted/sample1.bam aligned/sample1.bam

Notes#

  • The workflow file is optional; if not specified, auto-discovery searches for main.oxoflow first, then any *.oxoflow file alphabetically
  • If no .oxoflow file is found, an error message suggests running oxo-flow init to create one
  • No shell commands are executed — the dry-run is read-only
  • Shell command previews are truncated to 80 characters
  • The environment type (conda, docker, etc.) is shown for each rule
  • Thread and resource settings are displayed per rule
  • Use dry-run to verify your workflow before committing compute resources
  • When --target is specified, only the named rules and all rules they depend on (transitively) are shown — downstream rules are excluded