CellBender 0.2 or 0.3
The pipeline can run CellBender 0.2 (0.2.2) or 0.3 (0.3.2). Choose with --version; the default is 0.3.
nextflow run cellgeni/nf-cellbender -r main --samples samples.csv --version 0.2
Each version has its own module and container, so a run uses exactly one of them:
--version | Module | Container |
|---|---|---|
0.2 | cellgeni/cellbender/removebackground_v02 | quay.io/cellgeni/cellbender:0.2 |
0.3 | cellgeni/cellbender/removebackground_v03 | quay.io/cellgeni/cellbender:0.3 |
Which one to use
Use 0.3 unless you have a reason not to. It estimates the expected cells and total droplets itself, supports more feature types for --exclude_features, writes an HTML report and a metrics file per sample, and stores the soup fraction of each cell in its output.
Use 0.2 to reproduce or extend an analysis that was done with 0.2.
Options that only one version accepts
Validation rejects an option the chosen version would ignore, so a run never silently drops something you asked for.
| Option | 0.2 | 0.3 |
|---|---|---|
--cells / --droplets | Both or neither (neither means the mapper preset) | Either, both or neither |
--mapper_preset | Rejected: 0.2 always uses the preset unless both --cells and --droplets are given | Off by default; turn it on to estimate from the mapper output |
--exclude_features | Only All (excludes antibody capture) | A comma-separated list of feature types |
--estimator | Rejected | naive, map, mean, cdf or mckp (CellBender’s default is mckp) |
--force_empty_umi_prior | Rejected | Accepted |
--epochs, --fpr, --lr, --min_umi | Accepted | Accepted |
For example, --version 0.2 --estimator mean stops with:
* --estimator (mean): Expected null (`--estimator` is only available for CellBender 0.3)
--version 0.2 and --version "0.2" both work. On the command line Nextflow reads 0.2 as a number, and the pipeline accepts either form.
What changes in the outputs
Both versions write cellbender.h5, cellbender_filtered.h5, cellbender_cell_barcodes.csv, cellbender.pdf and cellbender.log into cellbender/<id>/. Only 0.3 adds cellbender_metrics.csv, cellbender_report.html and cellbender_posterior.h5.
In the QC report, the soup fraction comes straight from the 0.3 output. For 0.2 it is computed from the input matrix and can be NA; see QC report.