Nextflow module sharing #3

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1. krokicki commented on Jan 23, 2026

   

   krokicki

   on Jan 23, 2026

   Last edited by krokicki

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   • Our shared modules (currently outdated): https://github.com/BioImageTools/nextflow-modules
   • Sanger modules: https://github.com/cellgeni/nf-modules
   • Janelia modules: https://github.com/JaneliaSciComp/nextflow-modules

   Aggregator that makes the above searchable: https://bioimagetools.github.io/nf-module-aggregator

   👍React with 👍1Reacted by Tong LI
2. BioinfoTongLI commented on Jan 23, 2026

   

   BioinfoTongLI

   on Jan 23, 2026

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   Again thinking out loud:
   maybe we can implement a github issue template for new modules, which people should give an idea of the input/output details as much as possible.

   ❤️React with ❤️2Reacted by Konrad Rokicki and Christian Tischer
3. BioinfoTongLI commented on Jan 27, 2026

   

   BioinfoTongLI

   on Jan 27, 2026

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   Again thinking out loud: maybe we can implement a github issue template for new modules, which people should give an idea of the input/output details as much as possible.

   template uploaded. feel free to edit if you've noticed anything to change.

   🎉React with 🎉1Reacted by Konrad Rokicki
4. tischi commented on Jan 28, 2026

   

   tischi

   on Jan 28, 2026

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   Hi @krokicki,

   Thank you very much for this useful work!

   Do you know whether there could be also a way to list relevant (i.e. image analysis related) nf-core modules?

   Such as https://nf-co.re/modules/cellpose/
5. krokicki commented on Jan 28, 2026

   

   krokicki

   on Jan 28, 2026

   Last edited by krokicki

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   @tischi It's easy to add nf-core modules, but we need a way to identify what's relevant. One option is to hard code the specific modules we're interested in, like cellpose. Another might be to look for certain keywords in the metadata.
6. tischi commented on Jan 28, 2026

   

   tischi

   on Jan 28, 2026

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   On https://nf-co.re/modules/ one can type keywords, e.g. "image".

   Google AI suggests also API driven ways.
7. BioinfoTongLI commented on Feb 3, 2026

   

   BioinfoTongLI

   on Feb 3, 2026

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   I'd prefer searching the keywords in meta.yaml file, e.g. https://github.com/BioImageTools/nextflow-modules/blob/main/modules/bits/dask/terminate/meta.yml#L3