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.