[eduard-watchmaker]

Bumps bwamem3/index and bwamem3/mem to bwa-mem3 0.17.0, as suggested by @nh13 on nf-core/methylseq#638. It is faster and uses less memory under --meth.

Output changes:

• Bare --meth (bisulfite/EM-seq): scoring now defaults to --meth-scoring genomic (feat(meth)!: default EM-seq/bisulfite --meth-scoring to genomic fg-labs/bwa-mem3#756), so scores, MAPQ, NM and some placements change. The module tests record read sequences and headers rather than scores, so their snapshots only change in the version strings. ext.args = '--meth --meth-scoring collapsed' keeps the 0.16.0 output; this is now noted in the mem meta.yml.
• --meth=taps and plain DNA alignment: unchanged.
• Indexes: byte-identical to 0.16.0, plain and --meth, so existing indexes keep working.
• Under -u: alternative hits are now written as XB:Z instead of XA:Z. No nf-core component passes -u.

Changes

• bwamem3/index, bwamem3/mem: bwa-mem3 0.16.0 → 0.17.0, with new Seqera containers, conda lock files and meta.yml container entries (nf-core modules containers create).
• bwamem3/mem meta.yml: note on the new bare --meth scoring default and how to keep the old one.
• Module snapshots regenerated on linux/amd64; only the version strings change. The subworkflows that use these modules (fasta_index_dna, fasta_index_methylseq, fastq_align_dedup_bwamem3 and fastq_align_dna) pass against their existing snapshots, unchanged.

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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!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• 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.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test bwamem3/index --profile docker
    • nf-core modules test bwamem3/mem --profile docker
  • For subworkflows:
    • nf-core subworkflows test fasta_index_dna --profile docker
    • nf-core subworkflows test fasta_index_methylseq --profile docker
    • nf-core subworkflows test fastq_align_dedup_bwamem3 --profile docker
    • nf-core subworkflows test fastq_align_dna --profile docker

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