Patch invalid input index def

[pditommaso]

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
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Description

This PR address the issue #68.

The main problem was the index was not properly declared in the remap_to_hla process inputs declared.

I guess this was not done because the input it's not just a single index file, but multiple ones. To make things worse the yara_mapper uses the ugly approach to take as input params not a fake path name and using it to resolve all the dependant files e.g. hla_reference_dna.rid.limits, hla_reference_dna.sa.ind, etc.

I've fixed introducing the following params:

  base_index_type = 'dna'
  base_index_path = "$baseDir/data/indices/yara" 
  base_index_name = "hla_reference_$params.base_index_type"
``  


This is also related to https #76 since the PR removes the `index` params .

[apeltzer]

Looks good to me - once Chris is happy, I'm too :-)

HLAtyping would really need some updated I fear, template bump(s), new release - something for the hackathon I guess

[christopher-mohr]

Thanks a lot @pditommaso !

@apeltzer I talked to @ggabernet and we think it would make more sense to do the template bump before merging. What do you think?

[christopher-mohr]

nf-core linting fails because params are not part of the schema yet. Can we still merge it? I will make a separate PR to complete the schema...