Additional settings

Tool 2 has two additional settings that you can change: identity and coverage.

  • Identity is used to specify the minimum DNA identity (default: 75).
  • Coverage is used to specifiy the minimum DNA coverage (default: 0).

You can specify these settings in the same way that you specified the database by using:

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

The command will look like this: 

nextflow run tool_2.nf --customSeq 'xxx' --identity 'yyy' --coverage 'zzz'

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

Example 1

nextflow run tool_2.nf --customSeq 'cerys' --coverage '90'

Tool 2 will run using the cerys database, default 80% minimum DNA identity and 90% minimum DNA coverage.

Example 2

nextflow run tool_2.nf --identity '70' --coverage '75'

Tool 2 will run using the default test database, 70% minimum DNA identity and 75% minimum DNA coverage.