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New module - TD2 (added modules for td2.longorfs & td2.predict) #9475
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SPPearce
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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 |
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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/longorfsmodule for extracting longest ORFs from transcript sequences - Added
td2/predictmodule 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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This documentation over |
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 |
SPPearce
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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)
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
Co-authored-by: Simon Pearce <[email protected]>
FYI, the docs have been adjusted, thank you for your feedback: nf-core/website#3689 |
Hi @SPPearce , I tried it and |
Added new modules for TD2 -
longorfsandpredictCloses #9470
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda