Slide-Seq

This pipeline pre-configured for people working at the Francis Crick Institue. If you're not from the Crick, it should be easy to configure the pipeline for your system. Just modify these two files:

• nexflow.config
• conf/process.config

Here is the documentation:

1. Pipeline structure
2. Pipeline configuration
3. Running the pipeline
4. Pipeline output
5. Troubleshooting

In a nutshell, first be sure that your singularity config directory is not in your home. For example:

$ ls -l ~/.singularity
lrwxrwxrwx 1 username domain users 40 Aug 26  2021 /camp/home/username/.singularity -> /camp/stp/babs/working/username/.singularity

Then, you can just run:

# load nextflow and singularity
module load Nextflow/22.04.0 Singularity/3.6.4

# pull the latest version
nextflow pull bahnk/SlideSeq -r main

# download example files
wget https://raw.githubusercontent.com/bahnk/SlideSeq/main/test/design.csv
wget https://raw.githubusercontent.com/bahnk/SlideSeq/main/params.yml

# run the pipeline and pray
nextflow run bahnk/SlideSeq -r main -params-file params.yml --design design.csv

If it fails it's probably because your MODULEPATH is missing some locations, and/or because you don't have access to the BABS reference area (/camp/svc/reference/Genomics/babs).

If you're on NEMO, you need to create a configuration file named singularity.configwith the following content:

singularity {
	enabled = true
	runOptions = "-B /nemo --nv"
}

Then, pass this configuration file to nextflow when you run the pipeline:

nextflow -c singularity.config run bahnk/SlideSeq -r main -params-file params.yml --design design.csv

Any issues => nourdinebah@gmail.com. Cheers,

Comments

The decision was made not to perform deduplication with UMI-tools for now. Maybe this feature will be added later. If necessary, UMI-tools can be run afterwards anyway.