Raw2ometiff

[CaroAMN]

PR checklist

Closes #8015

• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

added a test Zarr directory because with GitHub raw i can only access individual files. Can change that if i / or someone has a better idea :)

[luiskuhn]

Looks good to me! in the same good shape as this related module: #7518

[luiskuhn]

it seems the linting error is also related to the OME channel: 'ome' is not one of ['bioconda', 'conda-forge'], as in this previous PR: #7518

@maxulysse , @mahesh-panchal could you help us out here?

[maxulysse]

minor comments

[luiskuhn]

minor comments

thanks!

[famosab]

small additions :)

[famosab]

This is still under development but maybe when this is released with more functions you could use this when updating the module in the future: https://github.com/nf-core/nft-tiff

[CaroAMN]

This is still under development but maybe when this is released with more functions you could use this when updating the module in the future: https://github.com/nf-core/nft-tiff

Yes that would be nice :)

[CaroAMN]

Ok i hope i didn't forget anything this time 😅

[famosab]

Now that I understood that you are going for ome.tiff and not .tiff (could have known from the module name haha) I added a couple more comments to be consistent :)

[CaroAMN]

Now that I understood that you are going for ome.tiff and not .tiff (could have known from the module name haha) I added a couple more comments to be consistent :)

makes sense 👍

[famosab]

🚀

[famosab]

@maxulysse Can you check again if your changes have been addressed?

[luiskuhn]

@CaroAMN congrats!