`oxo-flow info`#

Derive catalog metadata from a workflow file — the machine-checkable subset that the oxo-community catalog shows on every workflow page (including the Parameters table).

Usage#

oxo-flow info [OPTIONS] <WORKFLOW>

Arguments#

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

Options#

Option	Short	Description
`--format <FORMAT>`		Output format: `json` (default, machine-readable on stdout) or `text` (human-readable summary)

Output (JSON)#

{
  "name": "simple-variant-calling",
  "version": "1.0.0",
  "rule_count": 7,
  "tools": ["alignment", "fastp", "gatk", "qc"],
  "resources": { "max_threads": 16, "max_memory": "32G" },
  "environments": { "conda": 3, "singularity": 4 },
  "config": [
    {
      "key": "reference",
      "default": "/data/reference/GRCh38.fa",
      "value_type": "string",
      "used_by": ["apply_bqsr", "base_recalibrator", "bwa_align", "haplotype_caller"]
    }
  ],
  "sample_groups": [
    { "name": "samples", "samples": ["NA12878", "NA12891", "NA12892"] }
  ],
  "pairs": [],
  "references": [],
  "input_dirs": ["aligned", "dedup", "raw", "recal", "trimmed"],
  "output_dirs": ["aligned", "dedup", "qc", "recal", "trimmed", "variants"],
  "git_sha": "8f005dab60a0ce024acc5048885d88e246119b5c",
  "git_remote": "https://github.com/example/simple-variant-calling.git",
  "git_describe": "v0.23.2"
}

git_sha / git_remote / git_describe — the workflow's git identity when it lives inside a git repository: the HEAD commit SHA, the origin remote URL, and the nearest tag (git describe --tags --always, falling back to an abbreviated SHA on untagged history). All three keys are omitted entirely outside a git repository (never null), so catalog consumers can test presence directly. The SHA matches the workflow_git_sha recorded in run checkpoints (see Workflow Versioning).
config — every [config] parameter with its default value, its derived type (string / int / float / bool / array / table), the rules that reference it ({config.<key>} in shells, scripts, inputs, or outputs, plus brace-less config.<key> in when conditions), and — when the workflow comments the key — its description taken verbatim from the [config] section comments. Declared parameters (key = { default, type, … }) render their typed default from the declaration metadata. Keys sorted, rule lists sorted. Engine-injected keys are excluded — the run-time churn keys (samples_list, pairs_list, samples_*), the reference keyed-config values (config.<reference name> = its output), and the reference_dir-derived paths — config_keys carries the bare key list.
config[].description — optional; present only when the key is commented. A contiguous block of # lines immediately above the key line (no blank line in between) is the description, joined with newlines so the author's line structure is kept; a trailing # comment on the key line itself is the fallback. Empty # lines and pure decorator lines (# ----) are dropped. Banner lines (# --- section ---) act as section markers: dropped when the block also has regular text, otherwise kept with their dashes stripped. Comments inside multi-line values (e.g. # lines within an array) never associate, and comments above [config.<name>] subtable headers describe the table key itself. Include files contribute descriptions too (first definition wins; include failures are silently skipped).
tools — conda/mamba environment YAML stems and container image names (registry path and tag stripped), deduped and sorted.
resources — max threads/memory across rules on the defaults-applied view (the same value the engine uses at run time), in the winning rule's original string format.
input_dirs / output_dirs — the top-level directory of every rule input/output pattern, deduped and sorted. {config.key} placeholders are resolved against [config] first, so a config-routed output like {config.out_dir}/{sample}.txt reports out_dir's value. {sample} -style wildcards resolve per-sample at run time and are excluded.

Examples#

Inspect a workflow before running it#

oxo-flow info --format text workflow/rnaseq.oxoflow

Workflow: rnaseq v0.23.2
Rules: 44
Config keys: fasta = refs/genome.fa, reads_dir = test/fixtures/raw, ...

The text format prints the same derived fields as the JSON, one per line (Input dirs: …, Output dirs: …, …) — it is a rendering of the identical metadata, not a separate source.

Feed the catalog pipeline#

The oxo-community catalog derives its per-workflow Parameters tables from the JSON output and commits it as data/configs.json in the site repository — regenerated with scripts/regen-configs.py whenever a workflow changes.

oxo-flow info#