Make nextflow pipeline to run copyKAT and SCEVAN

Question

Make nextflow pipeline to run copyKAT and SCEVAN

grst opened this issue 3 years ago · comments

I feel rpy2 is unreliable, the R packages are cumbersome to install and a lot of additional dependencies. On top of that, the R methods are relatively slow compared to the infercnv algorithm in Python and it makes sense to run them in parallel on individual patients, potentially on HPC.

I would suggest to

remove the copykat function as it is currently from the package
build a small nextflow pipeline that
- takes an anndata object as input
- splits it up by patient (or whatever variable in obs)
- converts it to SingleCellExperiment
- runs copykat and or SCEVAN
- has the dependencies packaged as docker/singularity containers.
provide loader functions for the results of copykat and SCEVAN such that
the visualizations functions of infercnvpy can be used.

Yuanjian Huang · Answer 1 · Mon Jan 17 2022 11:46:42 GMT+0800 (China Standard Time)

Hello @grst
Any plan to add the tutorial of CopyKat to the website (https://icbi-lab.github.io/infercnvpy/tutorials/reproduce_infercnv.html)?
Thanks!
Best,
YJ

Gregor Sturm · Answer 2 · Mon Jan 17 2022 16:42:33 GMT+0800 (China Standard Time)

Eventually yes, but it's likely not going to happen soon (i.e. within the next few months). This is more of a side-project and I can't currently justify to spend more time on it.

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On Mon, 17 Jan 2022 at 04:46, hyjforesight ***@***.***> wrote: Hello @grst <https://github.com/grst> Any plan to add the tutorial of CopyKat to the website ( https://icbi-lab.github.io/infercnvpy/tutorials/reproduce_infercnv.html)? Thanks! Best, YJ — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVZRV4ODV73S5KQOVHWTNDUWOGK3ANCNFSM5KND7PVQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>