Metacache

[alxndrdiaz]

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/createtaxdb 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).

[alxndrdiaz]

@jfy133 Closed the previous PR, this new PR has the dev branch as target.

[alxndrdiaz]

The failed GitHub test could be related to tests/default.nf.test, the following command:

nf-test test tests/default.nf.test --update-snapshot

Fails with the following error message (nf-test 0.9.3, Nextflow 25.10.2, and openjdk version "24.0.2-internal" 2025-07-15):

Error: BUG! exception in phase 'semantic analysis' in source unit './createtaxdb/nf-test.config' Unsupported class file major version 68

A similar error has been reported in the nf-test repo: Failing to run on JDK 24.

[jfy133]

Odd... so you can't run the test locally @alxndrdiaz ?

Also I forogt to mention I put the development checklist on the website, https://nf-co.re/createtaxdb/2.0.0/docs/usage/usage/dev/

Maybe you can confirm you've been through it and checked everything before I dive in (I was hoping end of this week, but I just heard my kid is sick so might not be possible)

[alxndrdiaz]

Odd... so you can't run the test locally @alxndrdiaz ?

Also I forogt to mention I put the development checklist on the website, https://nf-co.re/createtaxdb/2.0.0/docs/usage/usage/dev/

Maybe you can confirm you've been through it and checked everything before I dive in (I was hoping end of this week, but I just heard my kid is sick so might not be possible)

No hurry. I will read the checklist in the meantime. The Nextlow tests work fine locally (nextflow run -resume . -profile test,docker --outdir test_output), but nf-test test tests/default.nf.test --update-snapshot fails with the error described above.

[jfy133]

OK when I get back to this I'll try and replciat ehte erro

[jfy133]

• I've updated the test snapshot (maybe try running nf-test clean @alxndrdiaz to see if it fixes it
• I've fixed a small bug in the output samplesheet

In the meantime, I will make the following changes (in addition to the comments below)

• Update CITATIONS.md
• Update the methods text
• Update the CHANGELOG
• Update the metro map

[jfy133]

Can you look through to make sure you agree with my changes @alxndrdiaz , and if you do I think we are ready - thank you very much for picking this up!

[alxndrdiaz]

@jfy133 LGTM, merging now