Problem running nextflow scenic multirun pipeline from a converted loom file

[mt98]

Hi,
I have this publically available csv file with scaled and raw counts for single cell data. I proceeded with converting it into a seurat object, then subsetting part of the seurat object based on a group.
This subsetted seurat object was converted into a loom file using SCopeLoomR (code below).

counts <- interferon_high@assays$RNA@data
metadata <- [email protected]

add_cell_annotation <- function(loom, cellAnnotation)
{
cellAnnotation <- data.frame(cellAnnotation)
if(any(c("nGene", "nUMI") %in% colnames(cellAnnotation)))
{
warning("Columns 'nGene' and 'nUMI' will not be added as annotations to the loom file.")
cellAnnotation <- cellAnnotation[,colnames(cellAnnotation) != "nGene", drop=FALSE]
cellAnnotation <- cellAnnotation[,colnames(cellAnnotation) != "nUMI", drop=FALSE]
}

if(ncol(cellAnnotation)<=0) stop("The cell annotation contains no columns")
if(!all(get_cell_ids(loom) %in% rownames(cellAnnotation))) stop("Cell IDs are missing in the annotation")

cellAnnotation <- cellAnnotation[get_cell_ids(loom),,drop=FALSE]
for(cn in colnames(cellAnnotation))
{
add_col_attr(loom=loom, key=cn, value=cellAnnotation[,cn])
}

invisible(loom)
}

loom <- build_loom("data/interferon_high.loom", dgem=counts)
loom <- add_cell_annotation(loom, metadata)
close_loom(loom)
[1] "Adding global attributes..."

[1] "Adding matrix..."
|======================================================================| 100%[1] "Adding column attributes..."
[1] "Adding default metrics nGene..."
[1] "Adding default embedding..."
[1] "Adding row attributes..."
[1] "Adding columns graphs..."
[1] "Adding row graphs..."
[1] "Adding layers..."
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
Default metric nUMI was not added because the input matrix does not seem to be the raw counts.

I proceeded with going forward with the loom file. Created in the config file
nextflow config vib-singlecell-nf/vsn-pipelines \ -profile loom,scenic,scenic_multiruns,scenic_use_cistarget_motifs,scenic_use_cistarget_tracks,hg38,singularity > scenic.config

The scenic.config file (attached) was changed in the following way:
##put data in

data {
loom {
file_paths = 'data/interferon_high.loom'
suffix = 'interferon_high.loom'
}
}

#change executor to slurm and add account
process {
executor = 'slurm'
withLabel:'compute_resources__.*|compute_resources__default' {
cpus = 2
memory = '60 GB'
time = '1h'
clusterOptions = '-A b1042'
}

Start to run this and get the error:
N E X T F L O W ~ version 21.04.3
Launching vib-singlecell-nf/vsn-pipelines [agitated_volhard] - revision: 721c42f889 [v0.25.0]
Argument of file function cannot be empty
-- Check script '/home/mks9338/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/main.nf' at line: 743 or see '.nextflow.log' file for more details

I am not sure why it is calling file function empty, any help would be appreciated. I think there might be a problem with my loom file potentially as it does not recognize my raw counts.