.gitignore
.gitlab-ci.yml
.readthedocs.yml
CulebrONT.sbatch
LICENCE
README.rst
pyproject.toml
setup.py
.github/workflows/python-package.yml
culebrONT/VERSION
culebrONT/__init__.py
culebrONT/_version.py
culebrONT/culebrONT-complete.sh
culebrONT/culebront_logo.png
culebrONT/global_variables.py
culebrONT/main.py
culebrONT/module.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/top_level.txt
culebrONT.egg-info/zip-safe
culebrONT/containers/Dockerfile
culebrONT/containers/Singularity.culebront_tools.def
culebrONT/containers/Singularity.report.def
culebrONT/install_files/cluster_config_SLURM.yaml
culebrONT/install_files/config.yaml
culebrONT/install_files/tools_path.yaml
culebrONT/install_files/config_test/config_A.yaml
culebrONT/install_files/config_test/config_AC.yaml
culebrONT/install_files/config_test/config_AP.yaml
culebrONT/install_files/config_test/config_APC.yaml
culebrONT/install_files/config_test/config_APCQ-CIRQ.yaml
culebrONT/install_files/config_test/config_APCQ.yaml
culebrONT/install_files/config_test/config_APQ.yaml
culebrONT/schemas/config.schema.yaml
culebrONT/schemas/tools_path.schemas.yaml
culebrONT/scripts/__init__.py
culebrONT/scripts/controllingMapping.py
culebrONT/snakeWrapper/__init__.py
culebrONT/snakeWrapper/edit_files.py
culebrONT/snakeWrapper/global_variable.py
culebrONT/snakeWrapper/install.py
culebrONT/snakeWrapper/run.py
culebrONT/snakeWrapper/snakeWrapper.py
culebrONT/snakeWrapper/usefull_function.py
culebrONT/snakefiles/Snakefile
culebrONT/snakefiles/assemblers.snake
culebrONT/snakefiles/circular.snake
culebrONT/snakefiles/correction.snake
culebrONT/snakefiles/polishers.snake
culebrONT/snakefiles/quality.snake
culebrONT/snakemake_scripts/Report.Rmd
culebrONT/snakemake_scripts/assembly-stats.py
culebrONT/snakemake_scripts/get_benchmark.py
culebrONT/snakemake_scripts/get_stats_busco.py
culebrONT/snakemake_scripts/get_stats_flagstats.py
culebrONT/snakemake_scripts/get_versions.py
culebrONT/snakemake_scripts/makerange.py
culebrONT/snakemake_scripts/rotateCircSeqs.R
culebrONT/snakemake_scripts/run_mauve.py
culebrONT/snakemake_scripts/tagCircSeq.R
culebrONT/snakemake_scripts/which_version.py
docs/Makefile
docs/requirements.txt
docs/source/ABOUT.rst
docs/source/FAQ.rst
docs/source/INSTALL.rst
docs/source/PROJECT.rst
docs/source/WORKFLOWS.rst
docs/source/click.rst
docs/source/conf.py
docs/source/index.rst
docs/source/SupplementaryFiles/CulebrONT
docs/source/_images/circular.dot
docs/source/_images/culebront_logo.png
docs/source/_images/culebront_logo2.png
docs/source/_images/nocircular.dot
docs/source/_images/quality.dot
docs/source/_images/report.png
docs/source/_images/schema_pipeline_global-CIRC.png
docs/source/_images/schema_pipeline_global-NOCIRC.png
docs/source/_images/schema_pipeline_global-QUALITY.png
docs/source/_static/logo.css