I've also had to add Sys.setenv(R_USER_CACHE_DIR="${task.workDir}/cache") to most of the R code, as it was trying to access a cache folder outside of the apptainer. Not sure it that's a bug or user error though

Could you please give me the command of your run?

“nextflow run nf-core/crisprseq --analysis screening --input $sampleSheet -profile apptainer\ --library $guideLibrary --outdir $output \ --contrasts $contrasts --rra TRUE \ -w work-rra” And the MLE pipeline needed the simple. I edited /users/anh524/.nextflow/assets/nf-core/crisprseq/modules/local/mageck/graphrra.nf for rra and mle also needed users/anh524/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R Otherwise the failed to write to /Users/anh524/.cache/R and died.