[BUG] There is no package called "SeuratObject"

[alefrol638]

Describe the bug
When I am trying to import a seurat rds file using "-profile seurat.rds" the pipelines stops with the error: "Unable to find the required package "SeuratObject".
To Reproduce
Steps to reproduce the behavior:

1. Configure with these options:

~/nextflow_21.04.3/nextflow config vib-singlecell-nf/vsn-pipelines \
    -profile seurat_rds,single_sample_scenic,scenic_use_cistarget_motifs,scenic_use_cistarget_tracks,hg38,singularity \
    > project_name.vsn-pipelines.complete.config

2. Run using this entry point:

~/nextflow_21.04.3/nextflow -C ../project_name.vsn-pipelines.complete.config \
    run vib-singlecell-nf/vsn-pipelines \
    -entry single_sample_scenic

3. See error:

Command error:
  WARNING: While bind mounting '/home/user/project/nextflow:/home/user/project/nextflow': destination is already in the mount point list
  WARNING: While bind mounting '/home/user/project/nextflow/results/work/79/c26ac4e78b9087536a982da5afdc31:/home/frolova/ageing/nextflow/results/work/79/c26ac4e78b9087536a982da5afdc31': destination is already in the mount point list
  WARNING: While bind mounting '/home/user:/home/user': destination is already in the mount point list
  Loading required package: SeuratObject
  Error in .requirePackage(package) : 
    unable to find required package ‘SeuratObject’
  Calls: @<- ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called ‘SeuratObject’
  Execution halted

Work dir:
  /home/user/project/nextflow/results/work/79/c26ac4e78b9087536a982da5afdc31

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line


Cannot append SCENIC loom to SCope loom because the IDs do not match.

 -- Check script '/home/user/.nextflow/assets/vib-singlecell-nf/vsn-pipelines/./src/scenic/main.nf' at line: 194 or see '.nextflow.log' file for more details

Expected behavior

Running the whole pipeline, from scanpy to scenic, with the expression matrix imported from the seurat rds file.

Please complete the following information:

• OS: Linux 4.18.0-305.12.1.el8_4.x86_64
• Nextflow Version: v.21.04.3
• vsn-pipelines Version: v.0.27.0