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nf-cellbender runs CellBender remove-background
on Sanger's farm22 for a whole table of samples, and then builds one QC report across all of
them. It takes CellRanger or STARsolo output folders, .h5 files or .mtx folders, from Lustre or
from iRODS. CellBender jobs run on the GPU queues.
samples.csv ──► (download from iRODS) ──► CellBender 0.2 or 0.3 ──► QC summary + PDF ──► MultiQC report
module load cellgen/nextflow/26.04.6
nextflow run cellgeni/nf-cellbender -r main --samples samples.csvsamples.csv has an id and a path column:
id,path
sample1,/lustre/scratch124/.../sample1/cellranger
sample2,/lustre/scratch124/.../sample2/outs/raw_feature_bc_matrix.h5
Results go to results/: one CellBender folder per sample in results/cellbender/, and the QC
report in results/qc_report/.
| Page | Read it when |
|---|---|
| Getting started | You are running the pipeline for the first time |
| CellBender 0.2 or 0.3 | You need to choose a CellBender version, or an option is rejected for your version |
| Cell and droplet counts | CellBender called too many or too few cells, or you have .h5/.mtx input |
| Data on iRODS | Your sample folders are on iRODS, or a download fails |
| GPU queues and costcodes | You want to run on cub22 or tiger22, or jobs pend on gpu |
| Reruns and failures | A run stopped part-way and you want to continue it |
| Parameters | You need the full list of parameters and what each accepts |
| Outputs | You want to know what each output file is |
| QC report | You are reading the QC report and want to know which samples to worry about |
| Troubleshooting | Something failed with an error message |
| Developers | You are changing the pipeline or its modules |
| Changelog | You want to know what changed between releases |