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FredHutch / crispr-screen-nf

Nextflow workflow for analyzing CRISPR screen NGS data
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nf-core-izing? #1

Open olgabot opened 3 years ago

olgabot commented 3 years ago

Hello! Is there any interest in nf-core-izing this pipeline to add e.g. params.json so the pipeline can be submitted from a GUI interface with nf-core launch or through Seqera Nextflow Tower? Warmest, Olga

sminot commented 3 years ago

Hi Olga! I think we would be very interested in nf-core-izing the pipeline! At the moment we've been developing this for internal use, but in the longer term it would be great to get it out to the larger community. Is this something that you'd be able to get us started with, either with a stub or by pointing us to the right set of docs?

Thanks for the help, Sam

sminot commented 2 years ago

@olgabot, now that this workflow is a bit more robust, it wouldn't be a bad candidate for nf-core-izing. That said, I haven't gone down that road before and so I'm not exactly sure how much effort would be entailed. Any interest in diving in together?

ieres-amgen commented 1 year ago

Not sure if this conversation ever continued, but this would be great and something I would potentially be happy to contribute to as well.

In particular, I would find the pipeline more broadly useful if the input format can be changed from comma-separated/wildcard pathing to take a design csv, similar to nf-core pipeline inputs. @olgabot, any chance there is any kind of guidance on how to accomplish that beyond the existing examples in other nf-core pipelines? Is it relatively trivial to modify the inputs as currently read here to get to that formatting, or would it be better to write entirely new code for reading the input? I generally am interested in learning more about utilizing nextflow and "nf-core-izing" nf pipelines, so would appreciate any resources you'd recommend along those lines as well.

Thanks! -Ittai