Additional settings

Tool 1 has two additional settings that you can change: identity and coverage.

  • Identity is used to specify the minimum DNA identity (default `80`).
  • Coverage is used to specifiy the minimum DNA coverage (default `80`).

You can specify these settings in the same way that you specified the database, as follows:

--identity 'yy'
--coverage 'zz'

The command will look like this: 

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

Substitute xxx +/ yy +/ zz with the actual parameter you wish to use.

Example 1

To run Tool 1 with the vfdb database, default 80% minimum DNA identity and 90% minimum DNA coverage.

nextflow run tool_1.nf --abricateDB 'vfdb' --coverage '90'

Example 2

To run Tool 1 with the default card database, 70% minimum DNA identity and 75% minimum DNA coverage.

nextflow run tool_1.nf --identity '70' --coverage '75'

Example 3

To run ALL strains using Tool 1 with the resfinder database and 95% minimum DNA identity.

nextflow run tool_1_EVERYTHING.nf --abricateDB 'resfinder' --identity '95'