pipeline for the analysis of Spatial Transcriptomics data generated from our custom microarray
- singularity/apptainer
- Nextflow
- Pytorch
- Nvidia Cuda
- clone the repository
git clone https://github.com/francops1722/ST_transcriptomics.git - Download containers
./build_containers.sh - Add all need paramters in the csvParams.config
- Load nextflow module
ml Nextflow/24.10.2 - Run pipeline
nextflow run ST_analysis.nf -c nextflow.config -with-dag ST_flowchart.png