Port to Nextflow while keeping old jobs/tasks

[vinjana]

Migrate the sophia and sophiaAnnotate jobs to Nextflow. Do not touch the jobs themselves more than is necessary to for the migration.

• Set up the NF project.
• Remove/renome RODDY_ variables
• Use the plugin XML to set up the default configuration for Nextflow.
• Migrate the resource requirements from the plugin XML into workflow.
• Only include the environment-modules based software stack in the migration

Use the https://github.com/DKFZ-ODCF/nf-bam2fastq workflow as an example, of how the workflow should look like in the end.