Merge branch 'master' into 'dev'

# Conflicts:
#   README.md
#   docs/README.md
#   docs/installation.md
#   docs/usage.md
#   functional_tests/README.md
#   functional_tests/functions.py
#   functional_tests/launch_example.sh
#   functional_tests/main.py
#   main.nf
#   nextflow.config