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Re-add optional vcf input for sample-specific database generation and search #377

@jonasscheid

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@jonasscheid

Description of feature

After decision to drop this feature temporarily #248 and to implement this feature we need to

  • Add an optional variant column in the input samplesheet
  • Copy the epytope module and vcf splitting logic from https://github.com/nf-core/epitopeprediction
  • Create a fasta containing mutated protein sequences
  • Concat sample-specific fasta with --fasta input
  • Generate decoys
  • Give comet the concatenated sample-specific fasta

Additionally, make sure if no vcf is provided, that the decoy database is generated only once

EDIT: Current vcf workflow is using nf-core/epitopeprediction --fasta_output and inject in mhcquant via --fasta param

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