Description

• Change multiple_sep to ;
• Simplify processing of multiple input arguments using a helper functions
• Use .fasta as an extension if --fasta is set, otherwise use .fastq
• Refactor processing of output arguments
• Write custom tests to better understand and check where different reads are going.

Issue ticket number

Closes #xxxx

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes