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update svdb to v2.12.0 - #12928

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ramprasadn merged 6 commits into
nf-core:masterfrom
ramprasadn:bumpsvdb2.12.0
Sep 11, 2026
Merged

update svdb to v2.12.0#12928
ramprasadn merged 6 commits into
nf-core:masterfrom
ramprasadn:bumpsvdb2.12.0

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@ramprasadn

@ramprasadn ramprasadn commented Sep 11, 2026

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PR checklist

Closes #XXX

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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 <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@ramprasadn
update svdb to v2.12.0
96ac140
@ramprasadn
svdb: add gzip/tar conda deps and rebuild container to fix singularit…
a1beacc 
…y CI

The bcftools_svdb Wave image was missing gzip and tar under singularity
(only present via the docker image's OS base layer), causing the
SVDB_MERGE stub test to fail with exit 127. Pin them explicitly.
@ramprasadn
Merge branch 'master' into bumpsvdb2.12.0
96d4e4b
@ramprasadn
ramprasadn marked this pull request as ready for review September 11, 2026 11:30
beatrizsavinhas
beatrizsavinhas reviewed Sep 11, 2026
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Comment thread modules/nf-core/svdb/query/tests/main.nf.test.snap Outdated
beatrizsavinhas
beatrizsavinhas approved these changes Sep 11, 2026
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@beatrizsavinhas beatrizsavinhas left a comment •
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Looks good! Thanks for updating the module! 🌟
Just make sure to sync the branch before merging.

@ramprasadn
ramprasadn added this pull request to the merge queue Sep 11, 2026
Merged via the queue into nf-core:master with commit 56155f7 Sep 11, 2026
151 of 163 checks passed
@ramprasadn
ramprasadn deleted the bumpsvdb2.12.0 branch September 11, 2026 14:20
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@ramprasadn @beatrizsavinhas