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@khersameesh24 khersameesh24 commented Nov 28, 2025

Added new modules for TD2 - longorfs and predict

Closes #9470

  • [️✅] 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
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  • [️✅] Remove all TODO statements.
  • [✅] Emit the versions.yml file.
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  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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@khersameesh24 khersameesh24 self-assigned this Nov 28, 2025
@khersameesh24 khersameesh24 added the new module Adding a new module label Nov 28, 2025
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Please look at swapping to using a topic channel to emit the version:
https://nf-co.re/blog/2025/version_topics

@khersameesh24
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Please look at swapping to using a topic channel to emit the version: https://nf-co.re/blog/2025/version_topics

Hi @SPPearce , I have resolved the concerns you mentioned in the comments, can you please go over them if everything's fine

@khersameesh24 khersameesh24 requested a review from Copilot December 4, 2025 20:57
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Pull request overview

This PR adds two new modules for TD2 (TransDecoder 2), a tool for identifying candidate coding regions within transcript sequences. The modules support the longorfs and predict functionalities of TD2.

  • Added td2/longorfs module for extracting longest ORFs from transcript sequences
  • Added td2/predict module for predicting coding regions using ORF data
  • Includes comprehensive test coverage with both standard and stub tests for both modules

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 6 comments.

Show a summary per file
File Description
modules/nf-core/td2/longorfs/main.nf Main process definition for TD2 LongOrfs functionality to extract longest ORFs from transcript sequences
modules/nf-core/td2/longorfs/meta.yml Metadata and documentation for the longorfs module
modules/nf-core/td2/longorfs/environment.yml Conda environment specification for td2 v1.0.6
modules/nf-core/td2/longorfs/tests/main.nf.test Test cases for longorfs module with standard and stub tests
modules/nf-core/td2/longorfs/tests/main.nf.test.snap Test snapshot data for longorfs validation
modules/nf-core/td2/predict/main.nf Main process definition for TD2 Predict functionality to identify coding regions
modules/nf-core/td2/predict/meta.yml Metadata and documentation for the predict module
modules/nf-core/td2/predict/environment.yml Conda environment specification for td2 v1.0.6
modules/nf-core/td2/predict/tests/main.nf.test Test cases for predict module with setup dependency on longorfs
modules/nf-core/td2/predict/tests/main.nf.test.snap Test snapshot data for predict validation

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@khersameesh24
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Please look at swapping to using a topic channel to emit the version: https://nf-co.re/blog/2025/version_topics

This documentation over topics is a bit misleading and needs an update

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SPPearce commented Dec 5, 2025

Please look at swapping to using a topic channel to emit the version: https://nf-co.re/blog/2025/version_topics

This documentation over topics is a bit misleading and needs an update

Can you be more specific? It is very new, so if you can say what isn't correct or clear that would be very helpful

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khersameesh24 commented Dec 5, 2025

Please look at swapping to using a topic channel to emit the version: https://nf-co.re/blog/2025/version_topics

This documentation over topics is a bit misleading and needs an update

Can you be more specific? It is very new, so if you can say what isn't correct or clear that would be very helpful

The section under versions_fastqc and the one under topics should be similar, that's how the linter understands it, this would be true in almost all cases. But in the documentation these sections do not match. So the meta.yml file screenshot can be updated.

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A minor change to the versions (and you can try using a val directly for the version string, I haven't done a topic with a hardcoded version as yet).
Please add some more ontologies too, definitely the FASTA one.
nf-core modules lint --fix may do some for you (see https://nf-co.re/blog/2025/modules-ontology#using-nf-core-helper-tools)

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SPPearce commented Dec 8, 2025

Please look at swapping to using a topic channel to emit the version: https://nf-co.re/blog/2025/version_topics

This documentation over topics is a bit misleading and needs an update

Can you be more specific? It is very new, so if you can say what isn't correct or clear that would be very helpful

The section under versions_fastqc and the one under topics should be similar, that's how the linter understands it, this would be true in almost all cases. But in the documentation these sections do not match. So the meta.yml file screenshot can be updated.

FYI, the docs have been adjusted, thank you for your feedback: nf-core/website#3689

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A minor change to the versions (and you can try using a val directly for the version string, I haven't done a topic with a hardcoded version as yet). Please add some more ontologies too, definitely the FASTA one. nf-core modules lint --fix may do some for you (see https://nf-co.re/blog/2025/modules-ontology#using-nf-core-helper-tools)

Hi @SPPearce , I tried it and val("${VERSION}") does not work. I think the meta.yml linter only understands eval("echo ${VERSION}")

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new module: TD2

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