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Migrate khmer/normalizebymedian to nf-test #8357

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Merged
merged 8 commits into from
May 7, 2025

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LouisLeNezet
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PR checklist

Closes #7603

  • 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

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@SPPearce SPPearce left a comment

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I feel we should change the module here to use prefix.
This module apparently hasn't changed since the mass repo reorganisation almost 2.5 years ago.

@github-project-automation github-project-automation bot moved this from Todo to In Progress in nf-test Migration Apr 23, 2025
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I suspect the tests could just use the basic fastq files too, rather than requiring SEQTK_MERGEPE first (but provided they work I guess they are fine)

@LouisLeNezet LouisLeNezet requested a review from SPPearce April 24, 2025 08:49
LouisLeNezet and others added 3 commits April 24, 2025 16:13
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
@LouisLeNezet LouisLeNezet requested a review from SPPearce April 24, 2025 17:25
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SPPearce commented May 7, 2025

Ok, I think it wants interleaved fastq files for paired ends, where read1 and read2 come next to each other in one file.
To be honest, that is a much more sensible format than the two seperate files that are standard, but that's bioinformatics for you ;)

@SPPearce SPPearce added this pull request to the merge queue May 7, 2025
Merged via the queue into nf-core:master with commit c2e58b8 May 7, 2025
27 checks passed
@github-project-automation github-project-automation bot moved this from In Progress to Done in nf-test Migration May 7, 2025
zachary-foster pushed a commit to zachary-foster/modules that referenced this pull request May 8, 2025
* Migrate to nf-test

* Update script

* Update meta

* Update modules/nf-core/khmer/normalizebymedian/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* Update modules/nf-core/khmer/normalizebymedian/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

---------

Co-authored-by: LouisLeNezet <louislenezet@gmaio.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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nf-test migration: khmer/normalizebymedian
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