First nf-core/sopa release

[quentinblampey]

New release PR after recent updates (moving processes to modules, and using -params-file instead of --configfile).

The conda tests are broken for two profiles because some processes require the installation of a specific command-line tool. It works well using docker or singularity though. Do you know how I could fix this? Or maybe prevent using conda for some specific profiles (e.g., baysor and proseg).

EDIT: actually, there is also an issue with singularity on test_cellpose. This is due to a permission issue to write in the HOME directory. The lines below fixed the issue for Docker, but apparently not for Singularity...

withName: PATCH_SEGMENTATION_CELLPOSE {
    containerOptions = ''
}

Happy to hear from your review @mashehu @kenibrewer!

PR checklist

• 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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/sopa branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[quentinblampey]

Hi @mashehu and @kenibrewer,
Everything is ready on my side for the merge, should we proceed with the first release?

[mashehu]

Great job! Thanks for all your patience with all the back and forth, but this is looking very nice now!

[quentinblampey]

Awesome, thanks a lot @mashehu for the detailed review, I also think it looks much better now 😊

[mashehu]

aws_fulltest is failing... I am investigating it

[mashehu]

working for now

[mashehu]

and it failed https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3ISZkqZrFqbEal/logs (let me know if you can't access this)

[quentinblampey]

No, I received an Organization with name "nf-core" not found error. My seqera user name is quentin-blampey!

[quentinblampey]

Thanks, I now have access!
The dataset we used for the test_full doesn't contain a prior segmentation (old format), so I updated the pipeline parameters, it should run now

Does it also need a snapshot, or is it only checking that it runs successfully?

[mashehu]

it only tests a successful run (that will then be rendered on the website)