Refactor pipeline filtering, create params flags for tools

[slsevilla]

Changes

This PR includes the following changes:

• refactors filtering failed samples for fairy
• refactors ICA handling, terra handling
• add a param flags in nextflow.config
  • execution-based
    • run_busco
    • ncbi_excel_creation
    • extended_qc
    • run_srst2_mlst
    • run_griphin
  • feature-based
    • save_trimmed_fail
    • save_merged
    • save_output_fastqs
    • save_reads_assignment
• moves parameter checks upstream to main.nf
  • ICA
  • TERRA

Issues

This PR addresses the following issues:

• [x] fixes #147
• [x] fixes #149
• [x] fixes #150
• [x] fixes #151
• [x] fixes #153

Scope

These changes have only been tested on the --entry PHOENIX part of the pipeline, on an AWS EC2 instance.

Checklist

The following points were addressed in this PR:

• [x] Description of the changes with justifications and issue links, where applicable
• [x] Updated docs related to these changes
• [x] Updated CHANGE.md with changes outlined above and a reference to the PR number.

[slsevilla]

hey @jvhagey - this is ready for review!

[slsevilla]

Closing PR since updates listed here were submitted as separate commits / will not be updated.