Additional settings

Tool 3 has two settings that you can change: identity and core.

  • Identity is defined as the minimum percentage for blastp (default `95`).
  • Core is defined as the percentage of isolates a gene must be in to be core (default `99`).

You can specify these settings in the same way that you gave the job a name by using:

--perIdentity 'bbb' and/or --perCore 'ccc'

If both additional options are used, the format of the command is: 

nextflow run tool_3.nf --runID 'aaa' --perIdentity 'bbb' –-perCore 'ccc'

Substitute aaa +/ bbb +/ ccc with the actual parameter you wish to use.

Example 1

nextflow run tool_3.nf –-runID 'meredith'

Tool 3 will run using the default 99% core and default 95% minimum identity for blastp, and name the output folder meredith.

Example 2

nextflow run tool_3.nf –-runID 'maddox' --perCore '70'

Tool 3 will run using the default 95% minimum identity for blastp, 70% core, and name the output folder maddox.

Example 3

nextflow run tool_3.nf –-runID 'morgan' --perIdentity '90' --perCore '70'

Tool 3 will run using 90% minimum identity for blastp, 70% core, and name the output folder morgan.