Update databio/refgenie to 1.2.0

[github-actions]

Quarterly sync of databio/refgenie image pins from bulker/biobase,
produced by update_refgenie_crate.py from refgenie_crate_sources.yaml.

Do not merge without reading this

databio/refgenie is the only crate the refgenie-registry nightly
activates. Every tool whose version changes below renames the
assets that tool builds — refgenie derives the asset name from the
tool version — which forces a rebuild and orphans the S3 objects
published under the old name. hg38 and mm39 index rebuilds are hours
and tens of GB.

Before merging:

1. Check which changed tools appear in refgenie-registry/pep/samples.csv.
   Only those cost a rebuild tonight; the rest cost nothing until a
   recipe using them is queued.
2. Run refgenie-registry/tools/check_crate_coverage.py against the new
   manifest — it re-derives the required command set from the recipes.
3. Sanity-check each changed tool's custom_seek_keys.version
   expression still returns a non-empty, plausible version under the
   new image. A tool that reports an empty version does not fail
   loudly; it produces a garbage asset name.
4. Repoint databio/refgenie.yaml only when you want :default
   consumers to move. This PR does not touch the symlink.

Report

source crate : bulker/biobase_0.1.18.yaml
current crate: databio/refgenie_1.1.1.yaml

Sibling verification commands (run on a host with apptainer):
  apptainer exec docker://quay.io/biocontainers/hisat2:2.2.3--h8471819_1 which hisat2-build
  apptainer exec docker://quay.io/biocontainers/hisat2:2.2.3--h8471819_1 which hisat2-inspect
  apptainer exec docker://quay.io/biocontainers/bowtie2:2.5.5--h63e9258_1 which bowtie2-build
  apptainer exec docker://quay.io/biocontainers/bowtie:1.3.1--hb82490e_11 which bowtie-build
  apptainer exec docker://quay.io/biocontainers/htslib:1.24--ha79157c_0 which bgzip
  apptainer exec docker://quay.io/biocontainers/bismark:3.1.0--hfa8f182_0 which bismark_genome_preparation

Resolution:
  bedtools: exact match in biobase -> quay.io/biocontainers/bedtools:2.31.1--h13024bc_3
  bgzip: sibling of `tabix` -> quay.io/biocontainers/htslib:1.24--ha79157c_0
  bismark_genome_preparation: sibling of `bismark` -> quay.io/biocontainers/bismark:3.1.0--hfa8f182_0
  bowtie-build: sibling of `bowtie` -> quay.io/biocontainers/bowtie:1.3.1--hb82490e_11
  bowtie2-build: sibling of `bowtie2` -> quay.io/biocontainers/bowtie2:2.5.5--h63e9258_1
  bwa: exact match in biobase -> quay.io/biocontainers/bwa:0.7.19--h577a1d6_1
  epilog: override -> databio/epilog:latest
  gt: exact match in biobase -> quay.io/biocontainers/genometools-genometools:1.6.6--py311h21ec246_1
  hisat2-build: sibling of `hisat2` -> quay.io/biocontainers/hisat2:2.2.3--h8471819_1
  kallisto: exact match in biobase -> quay.io/biocontainers/kallisto:0.52.0--hd638d68_1
  mashmap: exact match in biobase -> quay.io/biocontainers/mashmap:3.1.3--pl5321hb4818e0_2
  pigz: exact match in biobase -> nsheff/pigz
  salmon: exact match in biobase -> quay.io/biocontainers/salmon:2.7.0--hfa8f182_0
  samtools: exact match in biobase -> quay.io/biocontainers/samtools:1.24--h9dcdb79_1
  STAR: exact match in biobase -> quay.io/biocontainers/star:2.7.11b--h5ca1c30_8
  tabix: exact match in biobase -> quay.io/biocontainers/htslib:1.24--ha79157c_0

Pin changes:
  bowtie2-build  quay.io/biocontainers/bowtie2:2.5.5--ha27dd3b_0
                 -> quay.io/biocontainers/bowtie2:2.5.5--h63e9258_1
  hisat2-build   quay.io/biocontainers/hisat2:2.2.2--h503566f_0
                 -> quay.io/biocontainers/hisat2:2.2.3--h8471819_1
  kallisto       quay.io/biocontainers/kallisto:0.52.0--h13ff97a_0
                 -> quay.io/biocontainers/kallisto:0.52.0--hd638d68_1
  salmon         quay.io/biocontainers/salmon:2.3.4--hfa8f182_0
                 -> quay.io/biocontainers/salmon:2.7.0--hfa8f182_0

Version changes (these RENAME published assets):
  hisat2-build   2.2.2 -> 2.2.3
  salmon         2.3.4 -> 2.7.0

(dry run) would write databio/refgenie_1.2.0.yaml