In an effort to improve maintainability and visibility, all tools and workflows have been updated using CWL v1.0 syntax, which has several beneficial side effects. Along those, there following features and improvements have been incorporated:

• [ChIP-seq] Remove narrow/broad peak pipeline division, report always both type of peaks instead
• [ChIP-seq] Report BAM files with duplicates both marked and removed
• [ChIP-seq] Run peak calling step for controls samples in ChIP-seq pipelines
• [ATAC-seq] Report percentage of mitochondrial reads
• Update deeptools reference to use latest 3.0.1 (some relevant syntax changes)
• Update json generator to produce jsons compatibale with the new implemented changes. Additionally:
  • All paths and constants are now configured in the consts.py file,
  • All options can be overwritten by command line arguments
• General code refactoring