Additional settings
Tool 4 has four parameters you can modify. To modify stringency use identity and/or eValue. To alter where the Tool looks for the input and output data use .
Modifying the search settings
Tool 4 has two additional settings that you can change: identity and eValue in the command line.
- Identity is used to specify the minimum DNA identity (default
90). - eValue is used to specifiy the minimum DNA eValue (default
1e-8).
You can specify these settings using:
--identity 'yy'
--eValue 'zz'
The command will look like this:
nextflow run tool_4.nf --identity 'yy' --eValue 'zz'
Substitute yy +/ zz with the actual parameter you wish to use. For example,
nextflow run tool_4.nf --identity '80' --eValue '1e-7'
Specifying different a input folders and/or reference library
Additionally, in the command line you can also specify an alternative input directory, and a alternative reference library.
| Term | Default |
|---|---|
--query ‘mmm’ |
vol-genomics/genome_tools/Tool_4/input_tool4/* |
--backgroundGenomesDir ‘nnn’ |
vol-genomics/genome_tools/reference_libraries/XXXXXXX |
Example
To deposit your output in a new subdirectory named 2022-04-29 use:
nextflow run tool_4.nf --output '/vol-genomics/genome_tools/Tool_4/output_tool4/2022-04-29'
Tip
If you are running the same script with altered parammeters you can add -resume to your command. The analysis will be quicker since it will use cached data. In this case it will used cached data for the first two steps (predictORFs and makeBLASTDatabase).