Seurat Integration fails due to future.globals.maxSize limit

[fhausmann]

Description of the bug

Running the integration using Seurat fails with the following error message:

  Place corrected count matrix in counts slot
  Set default assay to SCT
  Running SCTransform on assay: originalexp
  vst.flavor='v2' set. Using model with fixed slope and excluding poisson genes.
  Calculating cell attributes from input UMI matrix: log_umi
  Variance stabilizing transformation of count matrix of size 10000 by 25348
  Model formula is y ~ log_umi
  Get Negative Binomial regression parameters per gene
  Using 2000 genes, 5000 cells
  Error in getGlobalsAndPackages(expr, envir = envir, globals = globals) : 
    The total size of the 19 globals exported for future expression (‘FUN()’) is 1.14 GiB.. This exceeds the maximum allowed size of 500.00 MiB (option 'future.globals.maxSize'). The three largest globals are ‘FUN’ (1.12 GiB of class ‘function’), ‘umi_bin’ (19.25 MiB of class ‘numeric’) and ‘data_step1’ (7.97 MiB of class ‘list’)
  Calls: lapply ... getGlobalsAndPackagesXApply -> getGlobalsAndPackages
  Execution halted

Thank you for providing this pipeline!

Command used and terminal output

$ nextflow run -c ./nextflow.config -resume -work-dir work -profile singularity,gpu nf-core/scdownstream -r 85a3ca5 --outdir downstream --input samplesheet_downstream.csv -params-file params_downstream.yaml

Relevant files

No response

System information

Nextflow Version: 24.10.2
Hardware: HPC
Executor: Slurm
Container Engine: Singularity
OS: Ubuntu 24.04
Pipeline version: 85a3ca5
Profile: singularity,GPU