Update default Nextflow version to 26.04

[adamrtalbot]

This pull request updates the minimum required Nextflow version across documentation and CI workflows to ensure consistency and support for newer features. The changes also update the default and available Nextflow versions in workflow configuration files.

CI and workflow configuration updates:

• Updated the Nextflow version matrix in .github/workflows/ci.yml to test against versions 25.10 and 26.04, removing 25.04 from the matrix.
• Changed the default Nextflow version in .github/workflows/example.yml to 26.04 and added 26.04 to the list of selectable options.

Documentation updates:

• Updated the minimum required Nextflow version in docs/CONTRIBUTING.md and docs/getting-started/setup.md from 25.04.0 to 25.10.0 to reflect the new baseline. [1] [2]

[claude]

Code Review

The change is minimal: updates the default nextflow_version from 25.10 to 26.04 and adds 26.04 as a selectable option in the workflow dispatch inputs.

Tests: N/A — this is a CI workflow config change only.

Documentation/Examples: No updates needed for a version bump in a workflow file.

UX: The old 25.10 option is preserved, so existing manual runs aren't broken.

One observation: if 26.04 is now the default and recommended version, it may be worth checking whether the plugin's compatibility requirements (Java 11+, Groovy 3.x) have been validated against NF 26.04 before merging. If they have, LGTM.

[claude]

Code Review

This PR updates the supported Nextflow version matrix from [25.04, 25.10] to [25.10, 26.04] and raises the stated minimum in two docs files. The changes are broadly correct but there are three issues worth addressing.

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Findings

1. .github/workflows/example.yml line 42 — workflow_run fallback still hardcoded to 25.10

The manual-dispatch default was updated to 26.04, but the fallback used when the workflow runs automatically (triggered by CI via workflow_run) was not:

nextflow_version: ${{ github.event_name == 'workflow_dispatch' && fromJSON(format('["{0}"]', github.event.inputs.nextflow_version)) || fromJSON('["25.10"]') }}

Automated post-CI runs will always test against 25.10, silently skipping 26.04. The fallback string should be updated to "26.04".

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2. build.gradle line 8 — plugin manifest version contradicts updated docs

nextflowVersion = '24.10.0'

docs/CONTRIBUTING.md and docs/getting-started/setup.md now declare 25.10.0 as the minimum, but the plugin descriptor still advertises 24.10.0. Users on Nextflow 24.x–25.09.x will load the plugin without error (Nextflow trusts the manifest), yet the docs say they're unsupported. One of the two needs to match the other.

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3. CHANGELOG.md — [Unreleased] section not updated

The repo maintains a Keep-a-Changelog CHANGELOG.md with an empty [Unreleased] block. Dropping 25.04 from CI support and raising the stated minimum to 25.10.0 is a potentially breaking change for existing users and should be noted here.

[claude]

test comment to verify posting works

[claude]

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Code Review

This PR bumps the minimum supported Nextflow version from 25.04 to 25.10, adds 26.04 to the CI test matrix, and aligns docs and CI consistently. The changes are internally coherent — docs, CI, and the example workflow all agree on the new minimum.

Findings

1. AGENTS.md:35 — Stale CI matrix description (missed file)

AGENTS.md was not updated and still documents the old matrix:

CI is the source of truth for the supported matrix (Java 17/21, Nextflow 25.04/25.10) — see `.github/workflows/ci.yml`.

Should be updated to 25.10/26.04 to match the new ci.yml.

2. .github/workflows/example.yml:42 — Auto-trigger fallback still hard-codes 25.10 only

The manual-dispatch path correctly offers both 25.10 and 26.04 (with 26.04 as default), but the workflow_run auto-trigger fallback remains:

nextflow_version: ${{ ... || fromJSON('["25.10"]') }}

Automated runs triggered by workflow_run will never exercise 26.04. If the intent is to keep the example light-weight, this is acceptable — but worth a deliberate choice rather than an oversight.

[claude]

---

Code Review

This PR bumps the minimum supported Nextflow version from 25.04 to 25.10, adds 26.04 to the CI test matrix, and aligns docs and CI consistently. The changes are internally coherent — docs, CI, and the example workflow all agree on the new minimum.

Findings

1. AGENTS.md:35 — Stale CI matrix description (missed file)

AGENTS.md was not updated and still documents the old matrix:

CI is the source of truth for the supported matrix (Java 17/21, Nextflow 25.04/25.10) — see `.github/workflows/ci.yml`.

Should be updated to 25.10/26.04 to match the new ci.yml.

2. .github/workflows/example.yml:42 — Auto-trigger fallback still hard-codes 25.10 only

The manual-dispatch path correctly offers both 25.10 and 26.04 (with 26.04 as default), but the workflow_run auto-trigger fallback remains:

nextflow_version: ${{ ... || fromJSON('["25.10"]') }}

Automated runs triggered by workflow_run will never exercise 26.04. If the intent is to keep the example light-weight, this is acceptable — but worth a deliberate choice rather than an oversight.

[claude]

Code Review

This PR bumps the minimum supported Nextflow version to 25.10.0 and shifts the CI matrix to test 25.10/26.04, removing 25.04 coverage. All 7 changed files are internally consistent, and a CHANGELOG entry is present.

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Findings

.github/workflows/example.yml — option ordering vs default (minor UX)

The options list has "25.10" first but default: "26.04". GitHub Actions does respect the default: field for choice inputs (it will pre-select "26.04"), but convention is to list the default first so it is immediately visible in the dropdown. Consider swapping the order to put "26.04" first.

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build.gradle — pre-existing gap now resolved

The previous nextflowVersion = '24.10.0' was lower than the 25.04.0 minimum advertised in docs — a silent inconsistency. This PR aligns everything at 25.10.0. No further action needed; noted for context.

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Summary

Clean version bump with consistent updates across docs, CI, and the build manifest. The only actionable suggestion is reordering the options: list in example.yml to put "26.04" first since it is now the default.

[adamrtalbot]

Addressed Claude review in 98c2d7c:

• Updated AGENTS.md CI matrix to 25.10/26.04.
• Changed example.yml workflow_run fallback to 26.04.
• Aligned build.gradle nextflowVersion manifest to 25.10.0 (matches docs).
• Added CHANGELOG.md entry for the minimum-version bump.

NF 26.04 compatibility validated via CI matrix on this PR (all checks green).

[claude]

Code Review

This PR bumps the minimum supported Nextflow version to 25.10.0 and updates the CI matrix to test against 25.10 and 26.04. Documentation, CHANGELOG, AGENTS.md, and workflow files are all updated consistently — good coverage overall.

Two things worth addressing:

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build.gradle / docs inconsistency not acknowledged in changelog

The diff shows build.gradle changing from nextflowVersion = '24.10.0' to '25.10.0', but the docs being updated from 25.04.0 to 25.10.0. Before this PR, the enforced minimum (build.gradle) and the documented minimum (docs) were different. The CHANGELOG entry says 'Raised minimum supported Nextflow version to 25.10.0' without noting that the actual prior floor was 24.10.0 in practice. Users on 24.10.x-25.04.x could previously use the plugin despite the docs saying otherwise. Worth clarifying whether 25.10.0 is a breaking change relative to what was actually enforced.

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example.yml: default option listed second in dropdown

The options list in example.yml has '25.10' first and '26.04' second, but the default is '26.04'. GitHub Actions renders options in declaration order, so '25.10' appears at the top of the dropdown while '26.04' is pre-selected. Convention is to put the default first to avoid confusion for manual dispatches. Consider swapping the order.