feat(vamb/bin): add GPU support

[dialvarezs]

Same treatment SemiBin2 got in #12863, now for Vamb.

vamb/bin picks its container and conda environment from task.accelerator, carries the process_gpu label, and passes --cuda when an accelerator is declared. It also emits the CUDA runtime version to the versions topic.

Vamb pins torch ==2.6.0, which conda-forge only builds against CUDA 12.6, so that is what the GPU environment gets. That build has no sm_120 kernels, but the driver JITs the compute_90 PTX, so Blackwell cards still run.

The wave images are Amazon Linux based and ship neither find nor gzip, both of which the module used on its bins. So gzip joins the GPU environment and the find call becomes a null glob, which tolerates zero bins the same way.

Tests

The existing checks were closures without assert, so { path(...).exists() } and the Completed Vamb line were evaluated and discarded. Adding assert showed the log check never held, since the lines are timestamped.

The tests now use the metagenome binning dataset, which ships per-sample assemblies, BAMs and an abundance table, so BOWTIE2_BUILD, BOWTIE2_ALIGN, COVERM_CONTIG and MMSEQS_CONTIG_TAXONOMY all go. The taxonomy test keeps one GAWK, deriving the lineage from the contig labels the dataset documents.

What is asserted was measured over repeated runs. The bins, the cluster tables and the log move between runs, so the bins are checked as a partition instead: every contig Vamb clustered appears in exactly one bin. abundance, composition and latent_encoding held steady, so they are snapshotted alongside the versions.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• Remove all TODO statements.
• Broadcast software version numbers to topic: versions
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• nf-core modules test vamb/bin --profile singularity

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