style(raw-reads): use the repo's 100-character line length

[corneliusroemer-agent]

Why

raw-reads-processing/pyproject.toml declares [tool.ruff.lint.per-file-ignores], and that alone makes it a ruff configuration root. Ruff does not merge configs across directories, so the package inherits nothing from the root ruff.toml — including its line-length = 100. It has been silently using ruff's default of 88.

That makes it the odd one out, and by accident rather than by choice:

package	line length	how
ena-submission, taxonomy	100	inherits root ruff.toml
ingest, preprocessing/nextclade	100	own ruff.toml, set explicitly
cli	88	own config, set explicitly — deliberate
raw-reads-processing	88	own config, never set — ruff's default

The practical cost is that running ruff format from the repo root, where the length is 100, does not reproduce what CI checks from inside the package. I hit exactly that on #7266: the check passed locally and failed in CI.

Worth noting the same inheritance gap applies to the lint rules — the package gets ruff's defaults rather than the root's extend-select list. The "test/**" = ["S101"] ignore that is already there is inert for that reason, since S is not selected. I have not changed that here; it would surface a batch of new findings and deserves its own decision.

What a reviewer should check

The reformat is mechanical (ruff format at the new width) and touches 8 files. Tests pass unchanged.

Note this overlaps #7266, which touches three of the same files. Whichever merges second will need a reformat — happy to rebase this one on top of that if you would rather land #7266 first.

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