Dev > Master

[drpatelh]

Many thanks to contributing to nf-core/chipseq!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

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 necessary, also make a PR on the nf-core/chipseq branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/chipseq/tree/master/.github/CONTRIBUTING.md

[maxulysse]

I think it'll be good to mention all the param changes in the CHANGELOG in a deprecated section.
cf: https://github.com/nf-core/sarek/blob/master/CHANGELOG.md#deprecated

And since we're not warning about all changes anywhere, I think it could also be good to have a similar warning message in the main.nf just in case someone is trying to use and old param.
cf: https://github.com/nf-core/sarek/blob/05c6e0b63251af83b9e7d5b259cec9e679fccf57/main.nf#L107-L113

[drpatelh]

I think it'll be good to mention all the param changes in the CHANGELOG in a deprecated section.
cf: https://github.com/nf-core/sarek/blob/master/CHANGELOG.md#deprecated

And since we're not warning about all changes anywhere, I think it could also be good to have a similar warning message in the main.nf just in case someone is trying to use and old param.
cf: https://github.com/nf-core/sarek/blob/05c6e0b63251af83b9e7d5b259cec9e679fccf57/main.nf#L107-L113

I think theres a fine line between bloating both main.nf with warnings and the CHANGELOG. You have to bear in mind that I have changed ~16 parameters 😓 Im happy to add this change to the top of the CHANGELOG in bold.

[ewels]

+1 for adding to the changelog and only there. Will hopefully have parameter linting soon anyway.. 😉 ✨

[drpatelh]

What do you think about adding a single line for this at the top of the relevant section i.e.

Change all parameters from camelCase to snake_case

as opposed to listing them all explicitly?

[maxulysse]

Your going to hate me, but I would list then all...

[drpatelh]

This ok now?
https://github.com/drpatelh/chipseq/blob/master/CHANGELOG.md#deprecated

[drpatelh]

Updated the atacseq pipeline appropriately too.

[ewels]

Had a quick read over and everything looks great 👍

[drpatelh]

Thanks you!! 👍

[maxulysse]

Looks fantastic!

[drpatelh]

Thanks @maxulysse . Ill merge in the changes from dev and release this on Monday then 👍