Workflow parameters should be passed via ext.args in conf/modules.config

[pinin4fjords]

I don't think all this stuff in the workflow file should be there. Rather we should be using ext.args in the conf/modules.config to pass the parameters through.

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/scflow pipeline documentation

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
2. See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:

Additional context