snakemake-cellranger

This is the Cellranger workflow for the Odomlab.

The pipeline and this documentation is work in progress and incomplete. Feel free to improve it by forking the repository and making a pull request.

Features

• Read OTP-exported metadata to gather sample information.
• Link FASTQ files as CellRanger compatible filenames
• Run CellRanger count for Gene Expression datasets.
• Store (subsetted) metadata CSV for downstream use.

Feature ideas

• Add Cellranger ATAC
• Add Spaceranger
• Create a Seurat object and store as Rdata file.
• Create a SingleCellExperiment object and store as Rdata file.
• Run MultiQC on available FastQC file.
• ...

How to get

Clone this repository.

On the DKFZ cluster, you need to use HTTPS because SSH connections are blocked by the proxy server.

To avoid typing your Github password each time, you may use Github's Personal Access tokens and store it in your Shell.

How to configure

There is an example configuration in config/config-test.yaml.

To adapt the workflow, make a copy of this file and adapt it to your needs.

Minimal changes needed are:

• Metadata: Path to a OTP-exported metadata in ["metadata"]["raw"]. Multiple files can be listed.
• Output directory: ["paths"]["output_dir"] - where the results should be stored

How to run

You may call the pipeline as follows in the directory where you cloned it.

snakemake --cluster "bsub -n16 -q verylong -R rusage[mem=200GB]" -p -j4 -c42 --configfile config/config-cluster.yaml --use-conda  --use-envmodules

• --cluster may change depending on the computational footprint of your analyses
• --configfile should point to your personal configuration