nextflow.config

params {  
  refFasta = "$launchDir/data/AnnotatedProteins.fsa"
  peptidesTab = "$launchDir/data/iedb.tab"
  taxon = 5833
  peptideMatchResults = "iedb.gff"
  results = "$launchDir/output"
  nonTaxaShortPeptideCutoff = 5
}
process {
  maxForks = 10

  withName: 'epitopeMapping:smallExactPepMatch:preprocess' {
    ext.kmer_size = 2
    ext.format = "sql"
  }
  withName: 'epitopeMapping:smallExactPepMatch:match' {
    ext.kmer_size = 2
    ext.num_mismatches = 0
  }

  withName: 'epitopeMapping:exactPepMatch:preprocess' {
    ext.kmer_size = 5
    ext.format = "sql"
  }
  withName: 'epitopeMapping:exactPepMatch:match' {
    ext.kmer_size = 5
    ext.num_mismatches = 0
  }


  withName: 'epitopeMapping:inexactForTaxaPeptidesPepMatch:preprocess' {
    ext.kmer_size = 3
    ext.format = "pickle"
  }
  withName: 'epitopeMapping:inexactForTaxaPeptidesPepMatch:match' {
    ext.kmer_size = 3
    ext.num_mismatches = 1
  }


}
includeConfig "$baseDir/conf/docker.config"