feat: add dorado/aligner module

[sahuno]

Description

Adds dorado/aligner — a wrapper around Oxford Nanopore's dorado aligner, which uses minimap2 under the hood to align unaligned ONT BAMs (e.g. produced by dorado/basecaller) while preserving modified base tags (MM/ML) and other BAM auxiliary tags.

CPU-only (no GPU required) — dorado aligner wraps minimap2 which is CPU-native. GPU is only needed for basecalling.

Why a separate module from dorado/basecaller?

Follows nf-core convention of one tool-subcommand per module. This is also the approach recommended by @Kevin-Brockers / @dialvarezs in #11122 (dorado/basecaller review). Keeping basecall and align separate lets users:

• Use different CPU/memory profiles (basecall needs GPU, aligner doesn't)
• Swap the aligner for minimap2/align if preferred
• Resume the pipeline from the aligner step without re-basecalling

Test data

Test paths depend on nf-core/test-datasets#1969 (unaligned HG002 GIAB 10-read BAM). Tests were verified locally against the same files before PR; CI will go green once #1969 merges.

Verified real-test output:

[info] Running: "aligner" "--threads" "2" "genome.fasta" "HG002_PAW70337_giab_10reads.unaligned.bam"
[info] > Reads written: 10
[info] > total/primary/unmapped 21/6/4
[info] > Finished in (ms): 107

Snapshot strategy

Real-test snapshot intentionally captures only filename + dorado version (not BAM MD5), because dorado aligner embeds absolute paths in @SQ UR: and @PG CL: BAM header lines — these vary between test environments. Stub-test snapshot uses full process.out (stable because all files are empty touch'd).

PR checklist

• Description of changes (above)
• New tool — followed module conventions (main.nf, meta.yml, environment.yml, tests/)
• Test data — uses files from Add ONT BAM and bedMethyl test data: HG002 GIAB 10-read subset (PAW70337) test-datasets#1969
• No TODO statements
• Versions broadcast via topic: versions
• Naming conventions followed
• Input/output options per guidelines
• Resource label: process_high (CPU/RAM scales with input)
• Container: docker.io/nanoporetech/dorado:shac8f356489fa8b44b31beba841b84d2879de2088e (ONTPL license — not on bioconda; vendor container pattern matches nf-core/parabricks)
• nf-core modules test dorado/aligner --profile singularity ✅
• nf-core modules lint dorado/aligner ✅ (2 expected warnings re: vendor Docker Hub image, same as dorado/basecaller)

Conda and Docker profile tests not yet run (dorado not on bioconda; Docker not available on my dev host — expecting CI to validate).

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