Moved custom Institutional configs to nf-core configs on github

[drpatelh]

Many thanks to contributing to nf-core/tools!

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

• [x ] This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

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

We can now centrally store and maintain custom configs that are specific to individual Institutions. Config files have been moved to nf-core/configs and will be pulled by nextflow before pipeline execution.

[apeltzer]

Suggested change

	## v1.3dev
	## v1.4dev

[drpatelh]

Sorry. Thats exactly what I meant!

[drpatelh]

How do you make these changes after merging @apeltzer? My naive brain is trying to work it out!

[apeltzer]

My bad - I've merged before really thinking as I thought the commit was fine and good (expect for these smallish typos). I guess just make a new PR with just these two then and I'll merge it in... sorry about that.

Normally you can simply click "accept" and thats it... :-)

[drpatelh]

No worries. I have fixed this in #214 whilst I was dealing with another issue.

[apeltzer]

Suggested change

	* Added parameter `--igenomesIgnore` so `igenomes.config` isnt loaded if parameter clashes are observed
	* Added parameter `--igenomesIgnore` so `igenomes.config` isn't loaded if parameter clashes are observed

[drpatelh]

Agreed!

[ewels]

Super nice work @drpatelh!

Please can you describe this change in CHANGELOG.md and also add some documentation about how it works in the template pipeline docs?

[drpatelh]

Sorry got started with some of this and had to prep for presenting the pipeline to our User Committee. Back to reality!

I did put some description in the CHANGELOG.md. Did I miss something?
https://github.com/nf-core/tools/blob/dev/CHANGELOG.md

Assuming you mean adding the parameters in here:
https://github.com/nf-core/tools/blob/dev/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/docs/usage.md

And a description here:
https://github.com/nf-core/tools/blob/dev/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/docs/configuration/adding_your_own.md

[drpatelh]

#219

Added some description as requested and a bunch of other stuff I had noticed whilst writing nf-core/atacseq

[ewels]

You did indeed add something to the changelog, correct. Not sure how I missed that, sorry!

For the docs I more meant something specifically describing that the configs are fetched from a separate repository and people can add their clusters their so that they're available for all pipelines.

[ewels]

Note to self: refresh half-written replies on GitHub before posting.

This is great! I will stop talking now.