FastQC:
   Per base sequence quality : per_base_quality.png
   Per sequence quality scores : per_sequence_quality.png
   Per base sequence content : per_base_sequence_content.png
   Per base GC content : per_base_gc_content.png
   Per sequence GC content : per_sequence_gc_content.png
   Per base N content : per_base_n_content.png
   Sequence Length Distribution: sequence_length_distribution.png
   Sequence Duplication Levels : duplication_levels.png
   Kmer Content : kmer_profiles.png
   Per tile sequence quality : per_tile_quality.png
   Adapter Content : adapter_content.png

Fileextension:
   fastq:
      - .fastq.gz
      - .fastq
      - .fq
      - .fq.gz
   bam:
      - .bam

Trimmomatic:
   illuminaClip_seedMismatch : 2
   illuminaClip_simpleClip : 10
   leading : 3
   trailing : 3
   trimOption : "SLIDINGWINDOW:4:20"
   trimBetter_threshold : 0.15

forAssembly.Illumina:
   trimBetter_threshold : 0.1
   trimOption : "SLIDINGWINDOW:4:25"

forAssembly.IonTorrent:
   trimBetter_threshold : 0.2
   trimOption : "SLIDINGWINDOW:4:15"

forMapping.Illumina:
   trimBetter_threshold : 0.15
   trimOption : "SLIDINGWINDOW:4:15"

forMapping.IonTorrent:
   trimBetter_threshold : 0.25
   trimOption : "SLIDINGWINDOW:4:15"
