Quick start commands

Deposit the assembled genomes of the strains you want to compare in the input folder.

Set up a stable connection:

tmux new -s <name>

To run Tool 1:

nextflow run tool_1.nf --abricateDB 'xxx'

Available databases

argannot, card, ecoh, ecoli_vf, ncbi, plasmidfinder, resfinder and vfdb

nextflow run tool_1.nf --abricateDB 'xxx' --identity 'yy' --coverage 'zz'

Example

nextflow run tool_1.nf --abricateDB 'resfinder' --identity '90' --coverage '75'

Tip

To view the Quick start instructions from the command line use:

nextflow run tool_1.nf --help