Utilities

Run script

The command line interface for Nextflow can become lengthy and tedious to type each time, due to the customization associated with routine pipeline runs, the lack of short form variable flags in Nextflow e.g. typing --nanopore_chemisty each time can be tedious.

A run script skeleton has been provided in the utils folder of mikrokondo (utils/mk_run.sh). Please customize the script to make it fit your usage, if you have issues running your modified script make sure it is executable by adding running chmod +x mk_run.sh.

Parameter file -params-file

You can also add a params file to the launch of Nextflow from the command line. More information is provided here