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nf-core / circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
https://nf-co.re/circdna
MIT License
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Circexplorer2 Annotate #54

Open uretaj opened 1 year ago

uretaj commented 1 year ago

Description of feature

Hello,

Would it be possible to add the annotate module of circexplorer2?

DSchreyer commented 1 year ago

Hi, thanks for this suggestion! I would for now keep circexplorer2 annotate out of the pipeline. It should not be hard to implement it, but I see it more like a downstream analysis tool which can be used by the user itself after running the pipeline.

Downstream analysis tools are mostly kept out of the pipelines as they can be distinctive for each use case.

I would suggest running annotate yourself with the output of nf-core/circdna circexplorer2.

I leave this issue open for now to see if other people also show strong interest in it.

Best regards, Daniel