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nf-core
[WIP] Add Institute-specific genomes!!
I have now tested this with the rnaseq pipeline (v3.0) on my own fork. This means we can have remote genome configs for each Institution so all users can just provide a --genome key from their own genomes.config and the files can be shared across all users saving the need to duplicate the data across your storage!!!
Since this file is on nf-core/configs if you have/add your Institutional profile here then these configs will be pulled dynamically when you run any nf-core pipeline meaning that if you update the genomes file here then that will be observed immediately for all users too i.e. saving the need to change this manually across multiple users.
Still fascinated that this repo is still working since we first put this together a couple of years ago. Being able to use remote genomes is now a massive bonus too!
I do like this idea.
I think you're only missing a bit more information in the crick.md file, like on the CAMP specific genomes ;-)
We will be adding more genomes in the future @MaxUlysse . I mainly want to get this in so users can test it properly. Will definitely add docs then 👍🏽 Also move the pipeline specific params as you suggested.
We will be adding more genomes in the future @MaxUlysse . I mainly want to get this in so users can test it properly. Will definitely add docs then 👍🏽 Also move the pipeline specific params as you suggested.
I'm afraid you also need to add the specific part in the rnaseq pipeline cf https://github.com/nf-core/configs/#adding-a-new-pipeline-specific-config.
So you can actually keep it the way it was until you make a new release ;-)
Done @MaxUlysse ! This custom rnaseq stuff has already been fixed for the next release anyway :)
@drpatelh Given this is 4 years old, I'm leaning towards closing it and asking oyu to start from scrach.
Will give you a week to think about it!
@drpatelh Given this is 4 years old, I'm leaning towards closing it and asking oyu to start from scrach.
Will give you a week to think about it!
I'd say we kill it