Fix ungrouped parameters

[beatrizsavinhas]

Description of feature

Description

Parameters snv_vcf, sv_vcf and custom_extra_files had been added to the code but not to the nextflow_schema. They were added to the nextflow_schema.json in #20 to fix the linting errors, but settings are missing for each parameter and the parameters are now ungrouped.

We need to refactor and add the necessary settings for these parameters.

For custom_extra_files, after discussion and comparison to code in nallo #50 (comment), we have concluded that there is no need to provide sample specific files to VEP and that the extra files necessary for plugins should be provided by the existing vep_plugin_files parameter. Parameter custom_extra_files should therefore be removed.

Acceptance criteria

• Description, format, pattern and check if exists is defined and the parameters are included in relevant groups in nextflow_schema.json.

• Settings for snv_vcf:

  "snv_vcf": {
      "type": "string",
      "pattern": "^\\S+\\.vcf(\\.gz)?$",
      "description": "<add_description>",
      "format": "file-path",
      "exists": true
  },
  

• Settings for sv_vcf:

  "sv_vcf": {
      "type": "string",
      "pattern": "^\\S+\\.vcf(\\.gz)?$",
      "description": "<add_description>",
      "format": "file-path",
      "exists": true
  },
  

• Remove unused parameter custom_extra_files.

[fevac]

@beatrizsavinhas adding the information should not need a refinement. We can add this for now and improve in the future. What VEP needs is extra testing to see if it works with and without this option (custom_extra_files) and general documentation (which would be part of your other PR)

[beatrizsavinhas]

@beatrizsavinhas adding the information should not need a refinement. We can add this for now and improve in the future. What VEP needs is extra testing to see if it works with and without this option (custom_extra_files) and general documentation (which would be part of your other PR)

I thought that the use of this parameter wasn't fully decided. But I've looked into the code and it seems that this parameter is only used for ENSEMBLVEP_VEP so I thought the name should be changed to vep_custom_extra_files. Updated acceptance criteria to reflect this.

On another note of the same song, the argument doesn't seem to be used in the module code at all (which I don't understand the reason why). So perhaps it's worth considering removing the parameter?

[fevac]

On another note of the same song, the argument doesn't seem to be used in the module code at all (which I don't understand the reason why). So perhaps it's worth considering removing the parameter?

No, we don't want to remove it, but then it should be fixed

[beatrizsavinhas]

On another note of the same song, the argument doesn't seem to be used in the module code at all (which I don't understand the reason why). So perhaps it's worth considering removing the parameter?

No, we don't want to remove it, but then it should be fixed

Decision to remove the parameter after further discussion in the PR #50 (comment).
Updated acceptance criteria.