nf-cellbender

Our cellbender repo but implemented in Nextflow.

There are two branches:

main — this branch contains the script for running cellbender on the FARM using Nextflow command line

nextflow-tower — this branch contains the script for running cellbender on the FARM using Nextflow Tower

Contents of Repo:

• main.nf the Nextflow pipeline that executes cellbender.
• nextflow.config — the configuration script that allows the processes to be submitted to IBM LSF on Sanger's HPC and ensures correct environment is set via singularity container (this is an absolute path). Global default parameters are also set in this file.
• examples/sample_table.tsv — an example of .tsv file containing path to cellranger output directory for each specified sample
• examples/sample_table_irods.tsv — an example of .tsv file containing IRODS path to starsolo output directory for each specified sample
• examples/run_cellranger_local_v2.sh — an example run script that executes the pipeline with --mapper cellranger and --version 0.2 options.
• examples/run_starsolo_irods_v3.sh — an example run script that executes the pipeline with --mapper starsolo and --version 0.3 options.
• docker/Dockerfile_v2 — a Dockerfile with image for cellbender of version 0.2.2
• docker/Dockerfile_v3 — a Dockerfile with image for cellbender of version 0.3.2

Pipeline Parameters:

Required parameters:

• --sample_table — Path to a .tsv file containing a list of sample IDs and paths to mappers result directory (see in example directory)
• --mapper — A mapper that was used to generate files (either cellranger or starsolo)
• --solo_quant — Quantification option for starsolo mapper (either Gene or GeneFull). only required if --mapper is starsolo

Optional parameters:

• --help — Display this help message
• --on_irods — Set this flag if the data is on IRODS
• --exclude_features — Specify a list of features to exclude. Available options include:
  • "Antibody Capture" — only available for --version 0.3 of cellbender
  • "CRISPR Guide Capture" — only available for --version 0.3 of cellbender
  • "Custom" — only available for --version 0.3 of cellbender
  • "Peaks" — only available for --version 0.3 of cellbender
  • "Multiplexing Capture" — only available for --version 0.3 of cellbender
  • "VDJ" — only available for --version 0.3 of cellbender
  • "VDJ-T" — only available for --version 0.3 of cellbender
  • "VDJ-T-GD" — only available for --version 0.3 of cellbender
  • "VDJ-B" — only available for --version 0.3 of cellbender
  • "Antigen Capture" — only available for --version 0.3 of cellbender
  • "All" — only available for --version 0.2 of cellbender
• --outdir — Output directory (default: cellbender-results)
• --cells — Number of cells (default: "cellbender-default")
• --droplets — Number of droplets (default: "cellbender-default")
• --epochs — Number of epochs (default: "cellbender-default")
• --fpr — False positive rate (default: "cellbender-default")
• --lr — Learning rate (default: "cellbender-default")
• --min_umi — Minimal UMI threshold (default: "cellbender-default")
• --version — Cellbender version (available: 0.2, 0.3; default: 0.3)
• --qc_mode — Quality control mode (default: 3)

Docker Image

The image is based on

FROM nvidia/cuda:12.1.1-cudnn8-runtime-ubuntu22.04

and includes installations of cellbender and R-4.4.2. The up to date image can be loaded from quay repository