2.0.0

Breaking change: Non-canonical chromosomes removed by defaults

Features:

• fair_genome_indexer update to 3.0.0
• fair_bowtie2_mapping update to 3.0.0
• snakemake-wrappers updated to v3.3.3
• snakemake github action updated to 1.25.1

Fix:

• Wrong parameters passed to MultiQC when importing pipeline with no parameters
• Report testing deactivated as long as TBD issue is opened at snakeamke

Documentation:

• Pipeline description updated
• Usage generalized
• Gustave Roussy users have a dedicated usage section