Merge branch 'dev' of gitlab.pasteur.fr:aperrin/pipeline_annotation into dev

.gitlab-ci.yml

PanACoTA/__init__.py

PanACoTA/align_module/get_seqs.py

PanACoTA/align_module/post_align.py

PanACoTA/annotate_module/general_format_functions.py

PanACoTA/annotate_module/genome_seq_functions.py

PanACoTA/bin/run_panacota.py

PanACoTA/pangenome_module/mmseqs_functions.py

PanACoTA/prepare_module/download_genomes_func.py

PanACoTA/prepare_module/filter_genomes.py

PanACoTA/subcommands/align.py

PanACoTA/subcommands/all_modules.py

PanACoTA/subcommands/annotate.py

PanACoTA/subcommands/corepers.py

PanACoTA/subcommands/pangenome.py

PanACoTA/subcommands/prepare.py

PanACoTA/subcommands/tree.py

PanACoTA/tree_module/fasttree_func.py

PanACoTA/tree_module/iqtree_func.py

PanACoTA/utils.py