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New module: xengsort/classify - #12864

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LeonHornich:xengsort_classify
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New module: xengsort/classify#12864
LeonHornich wants to merge 8 commits into
nf-core:masterfrom
LeonHornich:xengsort_classify

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@LeonHornich

@LeonHornich LeonHornich commented Sep 1, 2026

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Added new module xengsort/classify for classifying reads using a existing index file.

Notes:

  • apart from versions_xengsort, all output files are declared optional. This is due to the optional parameters --filter and --count. When specifying those a different set of files is produced.
  • in the nf-tests i only check for file creation since i got md5sum for empty file found error otherwise. I am assuming this is due to the minimum and small nature of the testing data

PR checklist

  • 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

@SPPearce SPPearce left a comment

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Are all your output files unstable? That doesn't seem great for the tool...
Can you use sanitizeOutput from nft-utils please.

@SPPearce SPPearce left a comment

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Why are all the output files unstable?

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