Run main from the Garnatxa launcher, pulled on every launch

[Paururo]

What changed and why

conf/garnatxa.sbatch asked for feat/gene-conversion, a branch deleted once it was merged, so Nextflow can no longer pull it. The template now runs main.

A branch also needs -latest. Nextflow keeps a clone of the project under ~/.nextflow/assets and, without it, runs the copy it cloned the first time, so a fix merged since does not arrive. The template now passes it.

Defaults and outputs

• REVISION defaults to main instead of feat/gene-conversion. To pin a run, set it to a release tag or a commit. Nextflow prints the commit it ran at the top of the driver log.
• The comment above REVISION said the report's provenance footer records the revision. The footer records the container, the references and the gene-conversion settings, so the comment now points at the driver log.
• Two small fixes in the same file. The log's Nextflow line printed the word "build" instead of the version, because nextflow -version prints version <X> build <N>. The usage message named SLURM's spooled copy of the script instead of the template.
• No pipeline code changes.

How it was verified

bash -n conf/garnatxa.sbatch                          # OK
shellcheck -s bash -S warning conf/garnatxa.sbatch    # clean
tests/run_tests.sh lint                               # clean
mkdocs build --strict                                 # passes

A dry run with stand-ins for module and nextflow submits nextflow run PathoGenOmics-Lab/BAMpiro -r main -latest -profile garnatxa -resume -ansi-log false --tsv samples.tsv --outdir results. The version line reads the number from a -version banner, and a missing samplesheet exits 2 with the template's name in the usage line. The template itself has not been submitted on Garnatxa from this branch.

Checklist

• tests/run_tests.sh passes locally (the lint leg; no Python or Nextflow code changed)
• ruff check . is clean, and I did not restyle code the change does not touch
• New or changed behaviour has a test (not applicable: the launcher has no test harness, the dry run above is the check)
• A new process in modules/ has a stub: block (not applicable: no new process)
• tests/data/ was not edited by hand (fixtures come from make_test_data.py)
• User-visible changes have a CHANGELOG.md entry and, where relevant, a docs update