save result object in h5ad format for better interoperability with other packages

[sreichl]

provide info in the docs e.g., resources but do not implement as the use cases are highly custom (which assays to put where etc.)

example code:

##converting to h5ad format
obj_m@active.assay <- "RNA"
                              
if(file.exists(file.path(analysis_dir, "merged", "rna_merged.h5Seurat"))) file.remove(file.path(analysis_dir, "merged", "rna_merged.h5Seurat"))                          
SaveH5Seurat(obj_m, filename = file.path(analysis_dir, "merged", "rna_merged.h5Seurat"))
                              
if(file.exists(file.path(analysis_dir, "merged", "rna_merged.h5ad"))) file.remove(file.path(analysis_dir, "merged", "rna_merged.h5ad"))                              
Convert(file.path(analysis_dir, "merged", "rna_merged.h5Seurat"), dest = "h5ad")

[sreichl]

or use this: https://github.com/theislab/anndata2ri

[sreichl]

or using SeuratDisk
add as a separate rule that does this for the last step?
or separate config that indicates step and assay(and data slot?) (breaking change)

# https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html

library("Seurat")
library("SeuratDisk")

# configs
object_path <- file.path("scrnaseq_processing_seurat/merged/NORMALIZED/object.rds")
results_path <- file.path("result/path")

dir.create(results_path, recursive = TRUE)

# load seurat object
data <- readRDS(file = file.path(object_path))

# save as h5Seurat
SaveH5Seurat(data, filename = file.path(results_path,"object.h5Seurat"), overwrite = TRUE)

# convert to anndata for scanpy (https://mojaveazure.github.io/seurat-disk/reference/Convert.html)
Convert(file.path(results_path,"object.h5Seurat"), assay = "SCT", dest = "h5ad", overwrite = TRUE)