Replacing delly call with delly sr module (delly v1.3.3 -> v2.6.0)

[gustav-001]

Description

Replaces the delly/call module with the new delly/sr module (delly v1.3.3 → v2.6.0),
and runs delly once per sample instead of once per SV type.

Why the SV type parallelization was removed

The delly flow previously ran delly 5× per sample (--svtype DEL/INS/INV/DUP/BND) and
stitched the results with BCFTOOLS_CONCAT. Both halves of that stop making sense under v2:

Delly v2 builds the VCF sample list from the variants it found
(src/modvcf.h:431, jctCountMap.size()), where v1.3.3 built it from the input BAMs
(src/modvcf.h:394, c.files.size()). So an SV type that yields no calls produces a BCF
with no sample column, and bcftools concat refuses to combine it with the others:
Different number of samples in test.DEL.bcf.

--svtype now defaults to ALL, which delly accepts explicitly (src/util.h:378).

Changes

• modules/nf-core/delly/sr/ installed, modules/nf-core/delly/call/ removed
• subworkflows/local/bam_variant_calling_delly/main.nf: DELLY_CALL → DELLY_SR with the
  new positional suffix input ("bcf"); sv_types fan-out, groupTuple(size:5) and
  BCFTOOLS_CONCAT removed
• conf/modules.config: --svtype dropped from ext.args; ext.prefix back to ${meta.id};
  BCFTOOLS_CONCAT block removed. --map-qual and --min-clique-size are unchanged — both
  still exist in v2.6.0
• CHANGELOG.md, docs/CITATIONS.md updated

Published output paths are unchanged (BCFTOOLS_SORT still writes ${meta.id}.delly),
so no tests/pipeline/* snapshot moved.

Testing

All green on --profile=+docker:

• tests/subworkflows/local/bam_variant_calling_delly — snapshot regenerated
• tests/subworkflows/local/bam_sv_calling — snapshot regen
• tests/default.nf.test — snapshot regenerated (merged VCF variantsMD5 moved, as expected
  for a caller version change)
• tests/pipeline/sv, tests/pipeline/bedpe, tests/pipeline/all_types — pass against
  existing snapshots, unchanged

PR checklist

• This comment contains a description of changes (with r
• If you've fixed a bug or added code that should be tested, add tests!
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes.
• Check for unexpected warnings in debug mode.
• CHANGELOG.md is updated.

[nvnieuwk]

One small comment, nice that the tool finally supports fully parallelization!. I'll approve once you've fixed the comment

[nvnieuwk]

Looks good! Thanks