JASEN

Json producing Assembly driven microbial Sequence analysis pipeline to support Epitypification and Normalize classification decisions

Setup

• git clone --recurse-submodules --single-branch --branch master https://github.com/genomic-medicine-sweden/JASEN.git
• Edit JASEN/nextflow.config
• Optionally run: bash JASEN/container/safety_exports.sh USER PREFIX

Singularity implementation

Image creation

• Install Singularity (through conda or whatever)
• cd JASEN/container && bash build_container.sh

Image execution

• singularity exec -B JASEN_INSTALL_DIR:/external -B WORKDIR:/out IMAGE nextflow -C /external/nextflow.config run /JASEN/main.nf -profile local,singularity

Conda implementation

• Install Conda ( https://www.anaconda.com/distribution )
• Install nextFlow ( curl -s https://get.nextflow.io | bash )
• bash JASEN/setup.sh
• nextflow run JASEN/main.nf -profile -local,conda