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Add metacache#682

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sofstam wants to merge 31 commits intonf-core:crazy-corgifrom
sofstam:add_metacache
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Add metacache#682
sofstam wants to merge 31 commits intonf-core:crazy-corgifrom
sofstam:add_metacache

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@sofstam
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@sofstam sofstam commented Feb 5, 2026

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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@sofstam sofstam marked this pull request as ready for review February 9, 2026 15:30
@jfy133 jfy133 changed the base branch from crazy-corgi to dev February 12, 2026 08:33
@sofstam sofstam changed the base branch from dev to crazy-corgi March 12, 2026 08:14
@jfy133
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jfy133 commented Mar 14, 2026

I've tried re-adding the missing MultiQC list of svg/png unstable files, which for some reason in your local dev environment your tests keep removing 🤔

@sofstam
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sofstam commented Mar 16, 2026

Now the tests are passing. Do you have any suggestion on how I could tackle the missing multiqc files?

@jfy133
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jfy133 commented Mar 16, 2026

Now the tests are passing. Do you have any suggestion on how I could tackle the missing multiqc files?

I think you need to look more closely at the .nf-test/tests/<hash>/output directory and log files to see what is causing MultiQC to fail

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sofstam commented Mar 16, 2026

Now the tests are passing. Do you have any suggestion on how I could tackle the missing multiqc files?

I think you need to look more closely at the .nf-test/tests/<hash>/output directory and log files to see what is causing MultiQC to fail

Right! I think we talked about that!

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From https://github.com/nf-core/taxprofiler/blob/dev/docs/usage/developing.md

Missing

  • Missing entry in assets/schema_database.json

Question

  • Has the full-test database sheet been updated?

TODO (later)

  • Update the metromap 😬

sofstam and others added 9 commits March 18, 2026 16:58
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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sofstam commented Mar 19, 2026

From https://github.com/nf-core/taxprofiler/blob/dev/docs/usage/developing.md

Missing

  • Missing entry in assets/schema_database.json

I can see metacache
https://github.com/sofstam/taxprofiler/blob/add_metacache/assets/schema_database.json#L26

Question

  • Has the full-test database sheet been updated?

https://github.com/nf-core/test-datasets/blob/taxprofiler/database_full_v1.3.csv

TODO (later)

  • Update the metromap 😬

@jfy133 jfy133 self-requested a review March 19, 2026 15:57
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3 participants