Run the Pipeline¶

To execute with Docker:

nextflow run main.nf -profile docker

To execute with Singularity:

nextflow run main.nf -profile singularity

To execute with the provided wrapper:

bash run_workflow.sh \
  -e <entry> \ #REQUIRED: arBASESPACE,arANALYSIS,DBProcessing,outbreakANALYSIS,outbreakREPORTING,NFCORE_OUTBREAK"
  -i <projectID> \ #REQUIRED: test
  -r <resumeRun> \ #OPTIONAL: Y,N (default Y)
  -o <outbreakReportFlag> #OPTIONAL: basic, advanced
  -n <nextflowParams> #OPTIONAL: nextflow configs (default -profile docker,test -entry NFCORE_ODHLAR --max_memory 7.GB --max_cpus 4)

Last update: 2025-01-29