Nextflow module sharing

[krokicki]

Discussion of Nextflow module sharing

@BioinfoTongLI @tischi

[krokicki]

• Our shared modules (currently outdated): https://github.com/BioImageTools/nextflow-modules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

[BioinfoTongLI]

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.

[BioinfoTongLI]

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.

[tischi]

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/

[krokicki]

@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.

[tischi]

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

Google AI suggests also API driven ways.

[BioinfoTongLI]

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