TODO.md

Things to do

• add FastQC
• add bamstats
• update genome and annotation names for views
• add preprocessing steps for input (fastq) and references (genome, annotation)
  • check chromosomes
  • check mate ids
  • add trimming and quality filtering step (e.g. cutadapt)
• allow for custom arguments in tool templates
• more flexible tool configuration
• add docker pull command as beforeScript to config
• add pipeline to CI server (circle)
• integrate Kallisto, Sailfish and maybe other mappers
• tune mapping steps for different quantification modes: only produce required bams
• autodetect sjdbOverHang for STAR index
• generate gff files from RSEM quantification
• use ext scope for task properties