New template update - 3_5_2

[BenjaminWehnert1008]

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/deepmutscan 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[mashehu]

@nf-core-bot fix linting

[MaximilianStammnitz]

@mashehu is there anything we can do here? We noticed that after some PR merges last week the website of the pipeline has now been "emptied", assuming there are some unresolved or new conflicts

[mashehu]

that with the website is a weird issue on our side. I keep trying to debug it, put don't find a clear reason what happens. sorry for that. Will try a clear build (usually fixes it)

[MaximilianStammnitz]

that with the website is a weird issue on our side. I keep trying to debug it, put don't find a clear reason what happens. sorry for that. Will try a clear build (usually fixes it)

looks like we're back online now :-)

[BenjaminWehnert1008]

@mashehu do you think this template update could be merged at this point? An approving review is still required.

And also, we have the test data now ready to push to the nf-core test data repository, but therefore still need a new branch for the pipeline. Could you help us with this, or should I write an additional message in the Slack channel?

Thanks!

[mashehu]

I will try to set it up later today. If I don't come back to you, please remind me tomorrow noon 🙂

[mashehu]

done https://github.com/nf-core/test-datasets/tree/deepmutscan

[mashehu]

you can merge, because this is pre-release (if you want I can even remove that requirement until you are closer to the release).

I might quickly try to fix the pre-commit linting errors, so you don't carry them with you and they are quite easy to fix.

[mashehu]

didn't see the auto-merge, but no worries about the linting