Problem 12

process '6C_ASE_knownSNPs' {
  tag "$sampleId"
  publishDir "$params.results/$sampleId"

  input:
      file genome from genome_file
      file index from genome_index_ch
      file dict from genome_dict_ch
      set sampleId, file(vcf), file(bam), file(bai) from grouped_vcf_bam_bai_ch

  output:
      file "ASE.tsv"

  script:
  """
  echo "${bam.join('\n')}" > bam.list

  java -jar $GATK -R ${genome} \
                  -T ASEReadCounter \
                  -o ASE.tsv \
                  -I bam.list \
                  -sites ${vcf}
  """
}