ITADN

CELLTYPES_SINGLER slows down the pipeline by using single CPU

#260Openkim-fehl 创建于 2026-03-11
bug
K
kim-fehlcommented
### Description of the bug When running tests on multi-cpu server I noticed that some steps are still using single cpu. Good example is `CELLTYPES_SINGLER`, it takes several minutes on each sample. I see in the docs that `SingleR()` function has `num.threads` parameter. As I can see, in `modules/local/celltypes/singler/templates/singleR.R` it is not utilized, although this process is labelled as `'process_medium'` ### Command used and terminal output ```console nextflow run nf-core/scdownstream -profile test,docker --outdir results -r dev ``` ### Relevant files _No response_ ### System information N E X T F L O W ~ version 25.10.4 nf-core/scdownstream 0.0.1dev Ubuntu 24.04, 10 CPU, 20 Gb RAM
1 条评论