Version 0.7.0

[0.7.0] - 2026-09-12

Added

• A reusable composite GitHub Action (action.yml) that wraps the
  nf-diff:diff verb for CI. It resolves the plugin from
  registry.nextflow.io (no build or plugins {} config needed), optionally
  sets up a JDK and Nextflow, runs the comparison against a project's existing
  .nextflow/history, uploads the report as an artifact, and can post/edit a
  Markdown pull-request comment. Typed inputs surface the common flags
  (last, run-a/run-b, format, fail-on-change, only/exclude,
  perf-threshold, the diff-* work-dir layers, verbose, dir,
  dir-a/dir-b, and published-a/published-b) with an extra-args
  passthrough, and it exposes report-path, html-report-path, artifact-url,
  artifact-id, exit-code, and identical outputs. When commenting on PRs
  with Markdown, it automatically generates and uploads the standalone HTML
  report dashboard and prepends a direct download link to the PR comment.
  The action honours the plugin's launcher contract —
  bare id (nf-diff:diff, never pinned) and inline --output= — and maps its
  exit codes so 1/2 fail immediately while 3 (runs differ +
  --fail-on-change) is deferred until after the report is uploaded and
  commented.

• A dogfood workflow (.github/workflows/nf-diff.yml) that generates two
  real runs from a trivial demo pipeline and compares them with the local
  action (uses: ./) on pull requests, exercising the action wiring
  end-to-end against the published plugin.

• An actionlint job in CI that lints every workflow (and shellchecks the
  embedded run-step scripts) via rhysd's official install script.

• The HTML report's "Resolved configuration" section now offers a git-style
  diff view alongside the table. The section is now a tabset with three views
  of the same resolved config: Table (the existing key / Run A / Run B
  grid, still the default), Full diff (every key as key = value lines,
  unchanged keys shown as context and changed keys shown as a - Run A / +
  Run B pair — keys present on only one side render a lone -/+), and
  Changes (the same diff with the unchanged context lines dropped). The diff
  reuses the report's existing .cl line-diff styling, so it inherits the
  colorblind-safe palette. The DAG section's tab machinery was generalized from
  .dag-tab* / data-dag to shared .tabset / .tab / .tab-panel /
  data-tab classes (with a single generic tab-switching script) so both
  sections drive off the same code. HtmlReportRenderer only; the Markdown /
  JSON / terminal renderers are unchanged.

• A new published-outputs layer compares two runs' result directories
  directly. Pass --published-a=<dir> and --published-b=<dir> to diff each
  run's outdir / publishDir tree instead of — or alongside — the per-task
  work-dir outputs (--diff-outputs). Files are keyed by their path relative to
  each published root and classified by size, then SHA-256 for same-size files,
  then a line-level diff for changed text files, reusing the same
  FileContentComparator engine as the work-dir layer. Symlinks are followed,
  so it works whether publishDir copied or symlinked. Unlike --diff-outputs,
  this reads the durable published results, so it still works after the work
  directories are gone (cleaned up, or on remote object storage). A published
  file change counts as a difference for isIdentical() / --fail-on-change.
  Implemented by PublishedComparator → DiffResult.PublishedDiff, wired
  through CompareOptions, DiffCommand, and RunComparator, and rendered by
  all four output formats (HTML, JSON, Markdown, terminal).

Fixed

• CommandParams.parse swallowed negative-number values (CommandParams.groovy)
  A flag whose value was a negative number (--min_log2fc -1.5, --seed -42, --scale -1e-3) was misread — the parser saw the leading -, treated the number as another option, and recorded the flag as boolean true. Now isNumericValue() recognizes signed decimals/integers/scientific notation as legitimate values. Impact: high — silently wrong parameter diffs for any pipeline using signed numeric params.
• DiffResult.failedExit counted the NO_EXIT sentinel as a failure (DiffResult.groovy)
  Nextflow writes Integer.MAX_VALUE to a task's exit field when it never produced one. The old check only excluded 0, so 2147483647 was treated as a non-zero failure. Now it excludes the sentinel explicitly. Impact: high — false-positive failures in the log/failure layers.
• Format.pctDelta dropped zero-baseline regressions (Format.groovy)
  A 0 → N change (a metric appearing from nothing) returned null and was silently discarded instead of ranking as a regression. Now 0→0 is 0.0 and 0→N is ±Infinity, with signedPct rendering it as ±∞%. Verified the threshold check and worst-first sort in RunComparator handle infinity correctly. Impact: medium.
• OutputComparator skipped nested files sharing a control-file name (OutputComparator.groovy)
  Control files (.command.sh, etc.) were matched by leaf name anywhere in the tree, so a genuine output like results/.command.sh was dropped. Now only work-dir-root entries (nameCount == 1) are skipped. Impact: low–medium.
• ConfigLoader.configFilesFrom could consume a following option as the -c path (ConfigLoader.groovy)
  A bare -c followed by another flag mis-consumed it, which could drop a real later -c config. Now it only consumes a non-- token. Impact: low.
• Duplicate java.nio.file.Path import (DagComparator.groovy) — cosmetic cleanup.
  Each fix has a dedicated regression test (new DiffResultTest.groovy plus cases added to FormatTest, CommandParamsTest, ConfigLoaderTest, OutputComparatorTest), and the full suite passes. Nothing is committed — the changes are staged in your working tree for you to review.

Full Changelog: v0.6.0...v0.7.0