Runs CellBender remove-background on Sanger's
farm22 for a table of samples, and builds one QC report across all of them. Inputs can be
CellRanger or STARsolo output folders, .h5 files or .mtx folders, on Lustre or on iRODS.
CellBender 0.2 and 0.3 are both supported and run on the GPU queues.
Documentation: https://cellgeni.github.io/nf-cellbender/
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, one row per sample:
id,path
sample1,/lustre/scratch124/.../sample1/cellranger
sample2,/lustre/scratch124/.../sample2/outs/raw_feature_bc_matrix.h5
Results are written to results/: CellBender output per sample in results/cellbender/, the QC
report in results/qc_report/. Run nextflow run cellgeni/nf-cellbender -r main --help for the
parameters.
| Page | |
|---|---|
| Getting started | First run, samples table, help and validation |
| Guides | CellBender 0.2 or 0.3, cell counts, iRODS, GPU queues, reruns |
| Reference | Parameters, samples table, outputs, QC report |
| Troubleshooting | Error messages and their fixes |
| Developers | Layout, modules, tests, releases |
The pages are also readable on GitHub in docs/.
| Path | Contents |
|---|---|
main.nf, workflow/ |
The pipeline |
nextflow.config, configs/ |
Global and per-process settings |
nextflow_schema.json, assets/ |
Parameter and samples table schemas, MultiQC config |
modules/cellgeni/ |
CellBender, QC and MultiQC modules, also published to the Nextflow registry |
examples/, resume/ |
Example samples tables and run scripts |
docker/ |
Dockerfiles for the CellBender images |
tests/ |
nf-test configuration and the LSF test runner |
docs/ |
Documentation site |
See the changelog.