[Paururo]

What changed and why

Three small fixes found while working on #13 and #14.

• Dead links in the docs. Eight links in five pages, and every page's Edit this page button (edit_uri in mkdocs.yml), pointed at indel-mask, a branch merged and deleted since. They now point at main, and every target was checked to exist there.
• HOME under the docker profile. The container runs as the invoking user (-u $(id -u):$(id -g)), who has no home in the image. So HOME was / and read-only: genmap, MultiQC and Java could not keep their settings, and software_versions.txt recorded genmap's mkdir error as its version (seen in the first end-to-end run of Run the pipeline for real in CI, on a cohort whose truth is known #14). The profile now adds -e HOME=/tmp.
• What aa_change holds in the SNP matrix. outputs.md said that where codon_change is filled, aa_change is what the base names alone. The first complete end-to-end run of Run the pipeline for real in CI, on a cohort whose truth is known #14 showed otherwise. By default the matrix reads FreeBayes' annotated raw VCF, where two changes of one codon on the same reads are one record annotated as the codon they make (CAC>GAG gives His145Glu on both bases). The page now says which VCF gives which, and the report's help no longer implies that a row's own change is per base.

Outputs and defaults

• Outputs: no change, except that under docker genmap's version is recorded rather than an error.
• Cluster runs: Singularity, and so every cluster profile, is untouched.

How it was verified

ruff check .                                                   # clean
python -m pytest tests/unit -q                                 # 2218 passed, 39 skipped
node --test tests/js/*.test.mjs                                # 120 passed
mkdocs build --strict                                          # passes; the built pages link edit/main/docs
python -m pytest tests/pipeline/test_container_scheme_per_profile.py -q   # 7 passed
nextflow config -profile local,docker .                        # runOptions = '-u $(id -u):$(id -g) -e HOME=/tmp'

• Not run: a real Docker run with the new HOME. The end-to-end job that would exercise it is in Run the pipeline for real in CI, on a cohort whose truth is known #14; once that merges, every pull request runs it.

Checklist

• tests/run_tests.sh passes: lint, unit and js locally; the pipeline leg in CI (a config-only change there, whose container tests pass locally)
• ruff check . is clean, and I did not restyle code the change does not touch
• New or changed behaviour has a test (not here: the HOME change is held by Run the pipeline for real in CI, on a cohort whose truth is known #14's end-to-end check on genmap's version once both are in)
• A new process in modules/ has a stub: block, and -profile test_full reaches it (not applicable: no new process)
• tests/data/ was not edited by hand
• User-visible changes have a CHANGELOG.md entry and, where relevant, a docs update