Merge branch 'dev' into 'dsl2'

# Conflicts:
#   README.md
#   bin/aln2taxaffi.py
#   conf/base.config
#   conf/test_genotoul_workq.config
#   docs/README.md
#   docs/installation.md
#   docs/usage.md
#   functional_tests/main.py
#   main.nf
#   nextflow.config
2 jobs for dsl2