Pipeline

Dependencies:

• Nextflow 25.04.7
• Miniconda 24.5.0

Usage:

nextflow run -profile conda LMonitor/main.nf --input [input samplesheet] --outdir [directory for output data]

Usage when adding new isolates to previous run:

nextflow run -profile conda LMonitor/main.nf --input [input samplesheet] --outdir [directory for output data] --partitions [reportree partitions file - 'cluster/reportree_out_partitions.tsv' in output folder] --schema [chewBBACA schema file - 'allelecall/schema' in output folder]

Visualisation dashboard

Dependencies:

• python 3.9.12
• dash 2.17.0
• plotly 5.22.0
• pandas 2.3.3

Usage:

python LMonitor/dashboard/dashboard.py [input .csv - 'cluster/full_data_cut.csv' in pipeline output folder]