@galaxy-foundry/summarize-nextflow

Statically introspect a Nextflow / nf-core pipeline tree and emit a JSON summary.

Source-specific (Nextflow), target-agnostic. The summary is the input to downstream Galaxy / CWL translation tooling. The output schema (summaryNextflowSchema) ships in this package at src/schema/summary-nextflow.schema.json and is exported alongside an AJV-backed validateSummary().

Status

v0.1.0 — initial public release. Local pipeline paths, remote git URLs, and --pin <tag|branch|sha> are all supported. A pinned or remote source is inspected from a detached temporary checkout outside the caller's repository; a caller-supplied checkout is never switched or reset, and source.url / source.version record the normalized remote and the resolved full commit SHA. See content/molds/summarize-nextflow/ and the Nextflow component research notes for design context.

Most consumers should install @galaxy-foundry/gxwf-foundry instead, which ships summarize-nextflow as a subcommand alongside the validators.

Install

npm install -g @galaxy-foundry/summarize-nextflow
# or, ephemeral:
npx --package @galaxy-foundry/summarize-nextflow summarize-nextflow <pipeline-path-or-url> [options]

Requires Node.js >= 20.

Usage

summarize-nextflow <path-or-url> \
  [--profile=test] \
  [--pin=<sha-or-tag>] \
  [--out=summary.json] \
  [--no-with-nextflow] \
  [--fetch-test-data] \
  [--test-data-dir=<dir>] \
  [--mulled-index-path=<multi-package-containers.tsv>] \
  [--no-validate]

Optional Nextflow integration

When nextflow is on PATH, summarize-nextflow shells out to nextflow inspect -format json and nextflow config -flat for fields only Groovy can resolve (per-process container under a profile, fully merged config). Pass --no-with-nextflow to force pure static parsing. See content/research/component-nextflow-inspect/index.md.

Output contract

JSON to stdout (or --out=). Stderr is human-readable progress. Exit codes:

• 0 — success
• 1 — input error (missing path, bad URL)
• 2 — resolution failure (network, missing dependency)
• 3 — schema validation failure
• 64 — not yet implemented (no input reaches this today)

License

MIT.