Running Tool 1

In order to run Tool 1 you need to enter two commands in the Terminal window.

First enter this command:

cd ~/genome_tools/Tool_1

Then enter this command. Replace xxx with the database you wish to search (keep the apostrophes):

nextflow run tool_1.nf --abricateDB 'xxx'

Specifying a database

The databases commands are: argannot, card, ecoh, ecoli_vf, megares, ncbi, plasmidfinder, resfinder and vfdb. Information about the databases can be found in the FAQs section.

Example

nextflow run tool_1.nf --abricateDB 'resfinder'

Tip

Tool 1 will use the default database if you do not include –-abricateDB 'xxx', which is card.

Running Tool 1 with ALL genomes

Tool 1 has a special feature that allows you to search ALL assembly files in the LIBRARY folder, rather than a selected subset in the tool1_input folder.

Simply use this command:

nextflow run tool_1_EVERYTHING.nf --abricateDB 'xxx'

Remember to specify which database you want to use, with --abricateDB 'xxx'. The default is card.