.gitignore
.gitlab-ci.yml
.readthedocs.yml
CHANGELOG.rst
GLOSSARY.md
LICENCE
README.rst
culebront_refactoring_specifications.md
pyproject.toml
.github/workflows/python-package.yml
ci/config_variants.py
culebrONT/__init__.py
culebrONT/_version.py
culebrONT/culebront_logo.png
culebrONT/global_variables.py
culebrONT/main.py
culebrONT/module.py
culebrONT/utils.py
culebrONT.egg-info/PKG-INFO
culebrONT.egg-info/SOURCES.txt
culebrONT.egg-info/dependency_links.txt
culebrONT.egg-info/entry_points.txt
culebrONT.egg-info/requires.txt
culebrONT.egg-info/scm_file_list.json
culebrONT.egg-info/scm_version.json
culebrONT.egg-info/top_level.txt
culebrONT/containers/Dockerfile_test
culebrONT/containers/apptainer.culebront_ltr.def
culebrONT/containers/apptainer.culebront_medaka.def
culebrONT/containers/apptainer.culebront_tools.def
culebrONT/install_files/config.yaml
culebrONT/install_files/configfile.yaml
culebrONT/install_files/tools_path.yaml
culebrONT/install_files/config_test/config_ecoli.yaml
culebrONT/install_files/config_test/config_yeast.yaml
culebrONT/schemas/config.schema.yaml
culebrONT/schemas/tools_path.schemas.yaml
culebrONT/scripts/__init__.py
culebrONT/scripts/controllingMapping.py
culebrONT/snakefiles/Snakefile
culebrONT/snakefiles/assemblers.snake
culebrONT/snakefiles/circular.snake
culebrONT/snakefiles/correction.snake
culebrONT/snakefiles/polishers.snake
culebrONT/snakefiles/pre_evaluation.snake
culebrONT/snakefiles/quality.snake
culebrONT/snakefiles/reported.snake
culebrONT/snakemake_scripts/Report.Rmd
culebrONT/snakemake_scripts/assembly-stats.py
culebrONT/snakemake_scripts/edit_quarto.py
culebrONT/snakemake_scripts/generate_samples.py
culebrONT/snakemake_scripts/generate_tools.py
culebrONT/snakemake_scripts/get_benchmark.py
culebrONT/snakemake_scripts/makerange.py
culebrONT/snakemake_scripts/rotate_circular.py
culebrONT/snakemake_scripts/tag_circular.py
culebrONT/snakemake_scripts/write_selection.py
culebrONT/snakemake_scripts/report_template/_quarto.yml
culebrONT/snakemake_scripts/report_template/cellalina.csl
culebrONT/snakemake_scripts/report_template/index.qmd
culebrONT/snakemake_scripts/report_template/offline.scss
culebrONT/snakemake_scripts/report_template/references.bib
culebrONT/snakemake_scripts/report_template/references.qmd
culebrONT/snakemake_scripts/report_template/report_helpers.py
culebrONT/snakemake_scripts/report_template/versions.csv
culebrONT/snakemake_scripts/report_template/_extensions/quarto-ext/lightbox/LICENSE
culebrONT/snakemake_scripts/report_template/_extensions/quarto-ext/lightbox/_extension.yml
culebrONT/snakemake_scripts/report_template/_extensions/quarto-ext/lightbox/lightbox.css
culebrONT/snakemake_scripts/report_template/_extensions/quarto-ext/lightbox/lightbox.lua
culebrONT/snakemake_scripts/report_template/_extensions/quarto-ext/lightbox/resources/css/glightbox.min.css
culebrONT/snakemake_scripts/report_template/_extensions/quarto-ext/lightbox/resources/js/glightbox.min.js
docs/Makefile
docs/requirements.txt
docs/adr/0001-pause-obligatoire-avant-quality.md
docs/source/CHANGELOG.rst
docs/source/CLI.rst
docs/source/CONFIGURATION.rst
docs/source/DEVELOPER.rst
docs/source/INSTALL.rst
docs/source/MIGRATION.rst
docs/source/QUICKSTART.rst
docs/source/RUNNING.rst
docs/source/TOOLS.rst
docs/source/conf.py
docs/source/index.rst
docs/source/SupplementaryFiles/CulebrONT
docs/source/_images/culebrontDOC.png
docs/source/_images/culebront_logo.png
docs/source/_images/culebront_logo2.png
docs/source/_images/report.png
docs/source/_static/logo.css