---
  ##############################################################################
  ### Annotation
  ##############################################################################
  other_RNAs_sequence: "../annotation/txome_rRNAs_joao.fa"
  other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
  transcripts_sequence: "../prepare_annotation/results/longest_pc_transcript_per_gene.fa"
  transcripts_index: "../prepare_annotation/results/longest_pc_transcript_per_gene.idx"
  transcript_id_gene_id_CDS: "../prepare_annotation/results/transcript_id_gene_id_CDS.tsv"
  ##############################################################################
  ### Output and log directory
  ##############################################################################
  output_dir: "results"
  local_log: "results/local_log"
  cluster_log: "results/cluster_log"
  dir_created: "results/dir_created"
  ##############################################################################
  ### sample info
  ##############################################################################
  input_dir: "samples"
  input_reads_pattern: ".fastq.gz"
  sample: ["example", "example2", "SRR1536304", "SRR1536305"]
  example: {adapter: GATCGGAAGAGCACA, minimum_quality: 20, quality_type: 33}
  example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64}
  SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
  SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
...