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Add module: pcangsd/inbreeding - #12587

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maxulysse merged 8 commits into
nf-core:masterfrom
ASendellPrice:pcangsd_inbreeding_coefficients
Aug 12, 2026
Merged

Add module: pcangsd/inbreeding#12587
maxulysse merged 8 commits into
nf-core:masterfrom
ASendellPrice:pcangsd_inbreeding_coefficients

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@ASendellPrice

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This PR adds a new module pcangsd/inbreeding for estimating per-sample inbreeding coefficients from genotype likelihoods using pcangsd.

PR checklist

Closes #12496

  • 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

@ASendellPrice ASendellPrice self-assigned this Aug 5, 2026

@erikrikarddaniel erikrikarddaniel left a comment

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Again a few comments from Claude.

Comment thread modules/nf-core/pcangsd/inbreeding/meta.yml Outdated
ASendellPrice and others added 2 commits August 12, 2026 06:27
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
@ASendellPrice

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@erikrikarddaniel, thanks for reviewing the PR. Not sure what is going on with the CI checks, but a lot more checks are running this time round. Looks like many of these are for other modules?

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@erikrikarddaniel, thanks for reviewing the PR. Not sure what is going on with the CI checks, but a lot more checks are running this time round. Looks like many of these are for other modules?

Strange. I have no idea, ask at Slack so @mashehu or someone can have a look.

@maxulysse
maxulysse added this pull request to the merge queue Aug 12, 2026
Merged via the queue into nf-core:master with commit 2b9ca5c Aug 12, 2026
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new module: PCANGSD/INBREEDING

3 participants