Make nextflow pipeline to run copyKAT and SCEVAN

[grst]

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.

[hyjforesight]

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

[grst]

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.

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

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