kingdoms does not need to be defined multiple times in workflows/autometa_flagged.sh

[jason-c-kwan]

Current Behavior

Since kingdoms is defined multiple times in workflows/autometa_flagged.sh, it is easily missed if a user wants to change the value of this variable

Steps to Reproduce

Expected Behavior

variable should be defined once in the script, and the value should then honored later in the script. Even better, it could be specified by user inputs with a default value.

Environment Information

autometa-config --print

Run Information

contents of nf-params.json

contents of .nextflow.log

Additional information