[Internal] [Bug] 'Not a valid path value:' for relative paths on command line

[jessicarowell]

Relative paths not being converted to absolute paths, resulting in an error. I believe it's a pretty high-level, not confined to one or two processes, but not part of the initial validation process. This might get corrected by the addition of a nextflow_schema.json.

Place an ❌ in a Box that Best Matches the Bug's Importance:

• [] 1 - Most severe (a full-break in core function)
• [] 2-4 - Moderate (break for a particular aspect/feature) (how integral is the broken feature?)
• 5 - Least severe (non-functional issue, such as inconsistency / error in documentation or administrative in nature) 

Please Complete the Following Information:

• OS: [e.g. iOS]:
• Browser [e.g. chrome, safari]:
• Version [e.g. 22]:
• Run environment (container, cloud service, HPC, platform, etc.):

Please Outline Necessary Steps to Replicate Bug (Go to.. Click on... Install the following... etc.):
nextflow run main.nf -profile test,singularity --species rsv --annotation false --submission true --output_dir test_rsv --submission_config conf/submission_config.yaml --meta_path ~/02.scratch/custom_test_metadata.xlsx --custom_fields_file ~/02.scratch/metadata_custom_fields.json

outputs error:
ERROR ~ Error executing process > 'TOSTADAS_WORKFLOW:TOSTADAS:INITIAL_SUBMISSION:SUBMISSION (1)'

Caused by:
Not a valid path value: 'conf/submission_config.yaml'

If you make --meta_path a relative path, you get the same error:
ERROR ~ Error executing process > 'TOSTADAS_WORKFLOW:TOSTADAS:METADATA_VALIDATION'

Caused by:
Not a valid path value: 'assets/custom_test_metadata.xlsx'

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Concrete Instructions to Resolve the Bug or Helpful Resources to Reference? Screenshots or Logs?