Update fasttree 2.1.10+galaxy1 to 2.1.10+galaxy3 in PathoGFAIR workflow.

[jmchilton]

Both intermediate releases are Galaxy-level bug fixes with no input/output changes:

• galaxy1→galaxy2: fix version_command (fix fasttree version command tools-iuc#3114)
• galaxy2→galaxy3: fix tool XML declaration (Fix fasttree tool tools-iuc#6640)

The toolshed doesn't have the version listed in the workflow anymore - looking over galaxyproject/tools-iuc#6640 I can imagine why. My first thought was maybe we broke the tool loading in galaxyproject/galaxy#15493. But that behavior was trying to block on a tool version. The problem isn't immediately clear but I could put more time into if want to push back and call this a tool shed bug - I could try to re-implement boolean parameters that have matching truevalues and falsevalues if they are empty.

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
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• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
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• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[jmchilton]

I guess the bot has an update that would have caught this with https://github.com/galaxyproject/iwc/pull/758/changes - but that change is a lot more expansive.

[jmchilton]

Note

Posted by Claude (AI assistant) on behalf of @jmchilton — not authored by them personally.

Superseded by #1293, which carries this fasttree bump forward onto current main and adds the test-schema regularization for this workflow (split out of #1286).

Two reasons for a fresh PR rather than a rebase:

1. This PR was incomplete. It updated content_id, tool_id, and changeset_revision on the fasttree steps, but left tool_version at 2.1.10+galaxy1 in all three. PathoGFAIR: fix unresolvable fasttree pin + test schema regularization #1293 fixes that.
2. The red here is unrecoverable. Combine chunked test results failed, which means a test failed — the Test workflows job reports success even when tests inside it fail, so its green tick was misleading. The artifacts and job logs from the 2026-03-19 run have since expired (410 Gone), so there is no way to recover which test failed.

Worth flagging for whoever picks up #1293: the fasttree pin is what stops PathoGFAIR from being invoked at all, so its workflow test has effectively never run on CI. Fixing the pin lets it execute for the first time, which is likely why this PR went red back in March — it probably surfaced a downstream failure that is normally masked. #1293 will give a fresh, readable signal.

The pin itself is confirmed still broken: the Toolshed's only installable fasttree revisions today are 2.1.10 and 2.1.10+galaxy3, and PathoGFAIR errors identically on main in the weekly runs of 2026-07-06 and 2026-07-13.