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:
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
).
Any issues => [email protected]
. Cheers,
The decision was made not to perform deduplication with UMI-tools for now. Maybe this feature will be added later.