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Migrate HLALA_TYPING to nf-test #8147

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LouisLeNezet wants to merge 6 commits into from
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Migrate HLALA_TYPING to nf-test #8147

LouisLeNezet wants to merge 6 commits into from

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@LouisLeNezet LouisLeNezet commented Mar 27, 2025

PR checklist

Closes #7578

  • 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 <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

@LouisLeNezet LouisLeNezet requested a review from a team March 27, 2025 08:55
@LouisLeNezet LouisLeNezet self-assigned this Mar 27, 2025
SPPearce
SPPearce reviewed Mar 27, 2025
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modules/nf-core/hlala/typing/main.nf
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@SPPearce SPPearce Mar 27, 2025

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These output paths all use meta.id, not prefix.

SPPearce
SPPearce reviewed Mar 27, 2025
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modules/nf-core/hlala/typing/main.nf
mv $graph graphs
mv graphs /usr/local/opt/hla-la/
mkdir $prefix
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@SPPearce SPPearce Mar 27, 2025

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Do we need this?

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@LouisLeNezet LouisLeNezet Mar 27, 2025

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Sorry the PR is not ready yet.
I have some trouble making it work.

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@LouisLeNezet LouisLeNezet Mar 27, 2025

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This staging might not be anymore needed if I found the way to make this module work 😢

SPPearce
SPPearce reviewed Mar 27, 2025
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modules/nf-core/hlala/typing/tests/main.nf.test.snap
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@SPPearce SPPearce Mar 27, 2025

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Snapshot is empty ;)

@LouisLeNezet LouisLeNezet marked this pull request as draft March 27, 2025 09:31
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LouisLeNezet commented Apr 10, 2025

There is an issue open on the github repository of HLALA but no answer yet.

DiltheyLab/HLA-LA#131

@SusiJo SusiJo mentioned this pull request Apr 16, 2025
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@LouisLeNezet LouisLeNezet mentioned this pull request Apr 16, 2025
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LouisLeNezet commented Apr 21, 2025

Migration done in #8328

@github-project-automation github-project-automation bot moved this from Todo to Done in nf-test Migration Apr 21, 2025
@LouisLeNezet LouisLeNezet deleted the typing branch April 24, 2025 07:44
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nf-test Migration
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nf-test migration: hlala/typing

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